scRNAseq Workflow
This workbook includes: 1. Creating a Seurat object from CellRanger output. 2. Preparing and cleaning the data a) Visualize QC b) Filter out unwanted cells c) Identify and remove doublets d) Normalization and scale e) Select Variable features 3. Merging and Harmonizing samples a) Merge samples b) Use Seurat find anchors to integrate c) Compare merged vs integrated 4. Dimensional reduction clustering and visualization a) PCA and component selection b) UMAP c) Clustering and visualization 5. Cluster annotation a) Visualize expression of known cell type markers b) Find cluster markers and look them up in reference cell type library c) Manual cluster annotation d) Decisions on merging clusters 6. Automated cluster annotation a) Seurat label transfer b) scClassify
Example data
We will use data from iPSC derived midbrain organoids There are two samples from dissociated midbrain organoids 1) iPSC line from a patient with Parkinson’s Disease carrying a triplication of the gene SNCA 2) The same iPSC line CRISPR corrected to make an isogenenic control
Analysis workflow
Load your required libraries. You need to have these libraries already installed.
Sys.time()[1] "2023-04-26 14:29:45 EDT"Warning message:
R graphics engine version 15 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed. library(Seurat)Registered S3 method overwritten by 'data.table':
method from
print.data.table
Registered S3 method overwritten by 'htmlwidgets':
method from
print.htmlwidget tools:rstudio
Attaching SeuratObjectlibrary(tidyverse)Registered S3 methods overwritten by 'dbplyr':
method from
print.tbl_lazy
print.tbl_sql ── Attaching packages ─────────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.2 ✔ purrr 1.0.1
✔ tibble 3.2.1 ✔ dplyr 1.1.1
✔ tidyr 1.3.0 ✔ stringr 1.5.0
✔ readr 2.1.3 ✔ forcats 0.5.2
── Conflicts ────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()library(DoubletFinder)
library(enrichR)Welcome to enrichR
Checking connection ...
Enrichr ... Connection is Live!
FlyEnrichr ... Connection is available!
WormEnrichr ... Connection is available!
YeastEnrichr ... Connection is available!
FishEnrichr ... Connection is available!
OxEnrichr ... Connection is available!library(clustree)Loading required package: ggraphlibrary("scClassify")
library(SingleCellExperiment)Warning: package ‘SingleCellExperiment’ was built under R version 4.2.2
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following object is masked from ‘package:dplyr’:
count
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts,
colCummaxs, colCummins, colCumprods, colCumsums, colDiffs,
colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs,
colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles,
colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates,
colVarDiffs, colVars, colWeightedMads, colWeightedMeans,
colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls,
rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts,
rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs,
rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs,
rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles,
rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates,
rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans,
rowWeightedMedians, rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Warning: package ‘GenomicRanges’ was built under R version 4.2.2
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:dplyr’:
combine, intersect, setdiff, union
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Warning: package ‘S4Vectors’ was built under R version 4.2.2
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:dplyr’:
first, rename
The following object is masked from ‘package:tidyr’:
expand
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Attaching package: ‘IRanges’
The following objects are masked from ‘package:dplyr’:
collapse, desc, slice
The following object is masked from ‘package:purrr’:
reduce
Loading required package: GenomeInfoDb
Warning: package ‘GenomeInfoDb’ was built under R version 4.2.2
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")',
and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Attaching package: ‘SummarizedExperiment’
The following object is masked from ‘package:SeuratObject’:
Assays
The following object is masked from ‘package:Seurat’:
Assayslibrary("Matrix")
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
The following objects are masked from ‘package:tidyr’:
expand, pack, unpackLoad the data: Starting with the control data.
# load data
# read in the data - CellRanger output - barcodes, features, expression matrix
# you need to enter the file path to the folder with the three files
con_data <- Read10X("/Users/rhalenathomas/Documents/Data/scRNAseq/AST23_BrainComm/CellRangerOuts/AST23isogenic/raw_feature_bc_matrix") |--------------------------------------------------|
|==================================================|#Look at the dimensions of the matrix
dim(con_data)[1] 33538 6794880#Look at a small part of the data
con_data[1:5, 1:5]5 x 5 sparse Matrix of class "dgCMatrix"
AAACCCAAGAAACACT-1 AAACCCAAGAAACCAT-1 AAACCCAAGAAACCCA-1
MIR1302-2HG . . .
FAM138A . . .
OR4F5 . . .
AL627309.1 . . .
AL627309.3 . . .
AAACCCAAGAAACCCG-1 AAACCCAAGAAACCTG-1
MIR1302-2HG . .
FAM138A . .
OR4F5 . .
AL627309.1 . .
AL627309.3 . .#Look at the distribution of the number of UMIs per cell
colSums(con_data) %>% summary Min. 1st Qu. Median Mean 3rd Qu. Max.
0.00 0.00 0.00 4.48 0.00 58329.00 #Look at the distribution of the number of genes per cell
colSums(con_data > 0) %>% summary Min. 1st Qu. Median Mean 3rd Qu. Max.
0.000 0.000 0.000 1.695 0.000 7999.000 Remove barcodes with too few genes that could be empty droplets
#Remove barcodes with less than 100 genes detected (you can select a different value here)
# without
con_data <- con_data[, colSums(con_data > 0)> 100]
dim(con_data)[1] 33538 3739colSums(con_data) %>% summary Min. 1st Qu. Median Mean 3rd Qu. Max.
106 2125 6243 7442 10872 58329 Filter genes and create a Seurat object
#We might not want to include genes that occur in few cells are no cells. Here we will filter out genes/transcripts that are in less than 3 cells.
# you don't have to filter any genes you can also change to any filter threshold you want
#Make a Seurat object
#Removing any genes detected in less than 3 cells
# we can also filter cells at this stage too.
con_seu <- CreateSeuratObject(con_data, project = "Control", min.cells = 3)
# look at the object dimensions
con_seuAn object of class Seurat
18557 features across 3739 samples within 1 assay
Active assay: RNA (18557 features, 0 variable features)Data distribution
# look at the distribution of total counts of RNA across cells
con_seu$nCount_RNA %>% summary Min. 1st Qu. Median Mean 3rd Qu. Max.
106 2125 6240 7441 10870 58316 # look at the distribution of unique RNA transcripts across cells
con_seu$nFeature_RNA %>% summary Min. 1st Qu. Median Mean 3rd Qu. Max.
101.0 997.5 2556.0 2433.6 3608.5 7981.0 Visualize the distributions
VlnPlot(con_seu, features = c("nCount_RNA","nFeature_RNA"), pt.size = 0)
Filter out unwanted cells
# Example cell filtering based on mitochondrial count percentage and number of UMIs ----------
#Calculate the percentage of RNA encoded mitochondrial genes from the mitochondrial DNA
con_seu <- PercentageFeatureSet(con_seu, pattern = "^MT-", col.name = "percent.MT")
con_seu$percent.MT %>% summary Min. 1st Qu. Median Mean 3rd Qu. Max.
0.000 2.257 4.783 8.075 8.524 94.762 VlnPlot(con_seu, features = "percent.MT", pt.size = 0.001)
Now we will filter some cells with too high mitochondrial RNA Filter out cells with too many RNA reads - these are likely doublets
#Remove any cells with more than 20% mitochondrial counts
con_seu.ft <- subset(con_seu, percent.MT < 20)
#Remove cells with very high UMI counts, which may be possible multiplets
con_seu.ft <- subset(con_seu.ft, nCount_RNA < 20000)
# see the results
VlnPlot(con_seu.ft, features = c("percent.MT", "nCount_RNA", "nFeature_RNA"), pt.size = 0.001)
# check how many cells we have
con_seu.ftAn object of class Seurat
18557 features across 3219 samples within 1 assay
Active assay: RNA (18557 features, 0 variable features)VlnPlot(con_seu.ft, features = "nFeature_RNA", pt.size = 0.001, y.max = 1000)Warning: Removed 2593 rows containing non-finite values (`stat_ydensity()`).
Warning: Removed 2593 rows containing missing values (`geom_point()`).
We might want to filter more cells with low total and/or unique RNA
# try some different filtering options
con_seu.ft <- subset(con_seu, percent.MT < 20)
dim(con_seu)[1] 18557 3739dim(con_seu.ft)[1] 18557 3392Apply final filtering conditions
con_seu_ft <- subset(con_seu, nCount_RNA < 60000 & nFeature_RNA > 500 &
percent.MT < 20)
dim(con_seu_ft)[1] 18557 2938Clear extra data object we don’t need anymore
rm(con_data,con_seu.ft)
Normalizing
# Normalize data (log normalization) and select genes with variable expression across cells --------------------------------------
con_seu_ft <- NormalizeData(con_seu_ft, normalization.method = "LogNormalize", scale.factor = 10000)Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|#Check out the effect of normalization
GetAssayData(con_seu_ft, assay = "RNA", slot = "data") %>% expm1 %>% colSums %>% headAAACCCAAGAGCTTTC-1 AAACCCACATTGACTG-1 AAACCCAGTTTGGAAA-1 AAACCCATCATCGACA-1
10000 10000 10000 10000
AAACGAAAGCCTGAAG-1 AAACGAAAGGAGAATG-1
10000 10000 GetAssayData(con_seu_ft, assay = "RNA", slot = "counts") %>% colSums %>% headAAACCCAAGAGCTTTC-1 AAACCCACATTGACTG-1 AAACCCAGTTTGGAAA-1 AAACCCATCATCGACA-1
8344 11697 8077 2877
AAACGAAAGCCTGAAG-1 AAACGAAAGGAGAATG-1
6219 6191 Finding Variable features
# three methods are available to choose variable features in this function
# our selection method is vst
con_seu_ft <- FindVariableFeatures(con_seu_ft, selection.method = "vst", nfeatures = 2000)Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|var <- VariableFeatures(con_seu_ft)
VariableFeaturePlot(con_seu_ft)
var[1:10] [1] "DLK1" "TTR" "CRYAB" "TAC1" "TPH1" "CENPF" "ANXA1" "LDHA" "GDF15" "TFPI2"Dimensionality reduction PCA and UMAP
#Scaling is recommended before PCA, as otherwise highly expressed genes will have a disproportionate effect on the PC composition
# we are also regressing MT genes to remove them from the PCA
con_seu_ft <- ScaleData(con_seu_ft, vars.to.regress = "percent.MT")Regressing out percent.MT
|
| | 0%
|
| | 1%
|
|= | 1%
|
|= | 2%
|
|== | 2%
|
|== | 3%
|
|=== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 5%
|
|==== | 6%
|
|===== | 6%
|
|===== | 7%
|
|====== | 7%
|
|====== | 8%
|
|====== | 9%
|
|======= | 9%
|
|======= | 10%
|
|======== | 10%
|
|======== | 11%
|
|========= | 12%
|
|========= | 13%
|
|========== | 13%
|
|========== | 14%
|
|=========== | 14%
|
|=========== | 15%
|
|=========== | 16%
|
|============ | 16%
|
|============ | 17%
|
|============= | 17%
|
|============= | 18%
|
|============== | 18%
|
|============== | 19%
|
|============== | 20%
|
|=============== | 20%
|
|=============== | 21%
|
|================ | 21%
|
|================ | 22%
|
|================= | 22%
|
|================= | 23%
|
|================= | 24%
|
|================== | 24%
|
|================== | 25%
|
|=================== | 25%
|
|=================== | 26%
|
|==================== | 26%
|
|==================== | 27%
|
|==================== | 28%
|
|===================== | 28%
|
|===================== | 29%
|
|====================== | 29%
|
|====================== | 30%
|
|======================= | 30%
|
|======================= | 31%
|
|======================= | 32%
|
|======================== | 32%
|
|======================== | 33%
|
|========================= | 33%
|
|========================= | 34%
|
|========================== | 34%
|
|========================== | 35%
|
|========================== | 36%
|
|=========================== | 36%
|
|=========================== | 37%
|
|============================ | 37%
|
|============================ | 38%
|
|============================= | 39%
|
|============================= | 40%
|
|============================== | 40%
|
|============================== | 41%
|
|=============================== | 41%
|
|=============================== | 42%
|
|=============================== | 43%
|
|================================ | 43%
|
|================================ | 44%
|
|================================= | 44%
|
|================================= | 45%
|
|================================== | 45%
|
|================================== | 46%
|
|================================== | 47%
|
|=================================== | 47%
|
|=================================== | 48%
|
|==================================== | 48%
|
|==================================== | 49%
|
|===================================== | 49%
|
|===================================== | 50%
|
|===================================== | 51%
|
|====================================== | 51%
|
|====================================== | 52%
|
|======================================= | 52%
|
|======================================= | 53%
|
|======================================== | 53%
|
|======================================== | 54%
|
|======================================== | 55%
|
|========================================= | 55%
|
|========================================= | 56%
|
|========================================== | 56%
|
|========================================== | 57%
|
|=========================================== | 57%
|
|=========================================== | 58%
|
|=========================================== | 59%
|
|============================================ | 59%
|
|============================================ | 60%
|
|============================================= | 60%
|
|============================================= | 61%
|
|============================================== | 62%
|
|============================================== | 63%
|
|=============================================== | 63%
|
|=============================================== | 64%
|
|================================================ | 64%
|
|================================================ | 65%
|
|================================================ | 66%
|
|================================================= | 66%
|
|================================================= | 67%
|
|================================================== | 67%
|
|================================================== | 68%
|
|=================================================== | 68%
|
|=================================================== | 69%
|
|=================================================== | 70%
|
|==================================================== | 70%
|
|==================================================== | 71%
|
|===================================================== | 71%
|
|===================================================== | 72%
|
|====================================================== | 72%
|
|====================================================== | 73%
|
|====================================================== | 74%
|
|======================================================= | 74%
|
|======================================================= | 75%
|
|======================================================== | 75%
|
|======================================================== | 76%
|
|========================================================= | 76%
|
|========================================================= | 77%
|
|========================================================= | 78%
|
|========================================================== | 78%
|
|========================================================== | 79%
|
|=========================================================== | 79%
|
|=========================================================== | 80%
|
|============================================================ | 80%
|
|============================================================ | 81%
|
|============================================================ | 82%
|
|============================================================= | 82%
|
|============================================================= | 83%
|
|============================================================== | 83%
|
|============================================================== | 84%
|
|=============================================================== | 84%
|
|=============================================================== | 85%
|
|=============================================================== | 86%
|
|================================================================ | 86%
|
|================================================================ | 87%
|
|================================================================= | 87%
|
|================================================================= | 88%
|
|================================================================== | 89%
|
|================================================================== | 90%
|
|=================================================================== | 90%
|
|=================================================================== | 91%
|
|==================================================================== | 91%
|
|==================================================================== | 92%
|
|==================================================================== | 93%
|
|===================================================================== | 93%
|
|===================================================================== | 94%
|
|====================================================================== | 94%
|
|====================================================================== | 95%
|
|======================================================================= | 95%
|
|======================================================================= | 96%
|
|======================================================================= | 97%
|
|======================================================================== | 97%
|
|======================================================================== | 98%
|
|========================================================================= | 98%
|
|========================================================================= | 99%
|
|==========================================================================| 99%
|
|==========================================================================| 100%
Centering and scaling data matrix
|
| | 0%
|
|===================================== | 50%
|
|==========================================================================| 100%con_seu_ft@assays$RNA@scale.data %>% dim[1] 2000 2938#Linear dimensionality reduction
#Choosing the number of PCs can depend on how many cells you have
con_seu_ft <- RunPCA(con_seu_ft, assay = "RNA", npcs = 30)PC_ 1
Positive: INA, DCX, NSG2, SYT1, BASP1, STMN1, NSG1, NREP, STMN2, IGF1
SOX4, PPFIA2, ANK3, MIR124-2HG, SLC8A1, CDH8, PKIA, GAD1, OLFM1, PRKAR2B
NNAT, CELF4, SNAP25, ATP1B1, CNTNAP2, SCN2A, SYNPR, CXADR, CSRNP3, ACSL4
Negative: PON2, GNG5, B2M, NTRK2, CD99, ZFP36L1, SPARC, SOX2, CLU, DBI
PMP2, ANXA5, CST3, CNN3, HLA-A, BCAN, PTN, NFIA, TTYH1, MPC1
GPM6B, TMEM123, PSAT1, CD9, CDK2AP1, PTPRZ1, CALU, MGST1, SOX9, SAT1
PC_ 2
Positive: EGLN3, CYSTM1, S100A6, FTL, EIF1, SELENOM, S100A10, PLOD2, SLIT2, PLA2G16
SQSTM1, FTH1, CD44, CRYAB, BNIP3, PTGDS, DDIT3, ANXA2, SAT1, GDF15
P4HA1, CLU, NPC2, NUPR1, MAP1LC3B, MGST1, TFF3, FOXA1, ATF5, ADGRV1
Negative: CDK1, MKI67, TOP2A, PBK, NUSAP1, CENPF, PCLAF, NUF2, UBE2C, RRM2
CCNA2, NDC80, SPC25, SGO1, ESCO2, TPX2, ZWINT, CENPU, NCAPG, KIF15
CKAP2L, ASPM, KIF11, PIMREG, KNL1, MELK, KIFC1, CENPK, DLGAP5, MIS18BP1
PC_ 3
Positive: NRXN1, MT-CO3, CSPG5, LINC00461, BCAN, OMG, VCAM1, PMP2, ST6GAL2, C1orf61
PTPRZ1, COLGALT2, LSAMP, LRRN3, SESN3, GABBR2, MSTN, MT-ND3, PTN, TFPI
MEIS2, LIX1, TTYH1, KCNQ3, SLC1A2, AQP4, CST3, LINC01896, NTRK2, ATP1B2
Negative: GDF15, ATF3, ATF5, S100A11, GADD45A, CDKN1A, ANXA2, EIF1, PPP1R15A, FTL
DDIT3, YBX3, SEC61G, TYMS, BTG3, ANXA1, CRABP2, GPNMB, S100A6, PLOD2
CLGN, LINC02154, TRMT112, TUBB6, CRYAB, KDELR2, TPT1, STC2, FTH1, ATF4
PC_ 4
Positive: ATF3, PPP1R15A, C1orf61, ATF5, CDKN1A, GADD45G, DLL1, GDF15, DDIT3, GADD45A
EGFR, LINC02154, AEN, ODC1, HIST1H2AC, GPNMB, PURPL, PMP2, SGCG, EIF1
TRBC2, GBE1, SESN2, PMAIP1, EDA2R, SERPINB8, HRK, HIST1H4H, IFRD1, SDCBP
Negative: KCNJ16, SLIT2, RSPO2, PEG10, ABCA8, NRN1, FOXA1, LGI1, CFC1, DCN
MSX1, SERTM1, PMP22, PLXDC2, C3orf58, COL21A1, KCNMB1, PDLIM5, SULF2, ASB4
EFNB3, TRABD2A, PTPRG, TFF3, PAMR1, CDO1, TMEM163, VAT1L, CPE, IGFBP5
PC_ 5
Positive: SOX14, SYNPR, IGF1, PRSS12, KIZ, SEMA3C, UNC13C, GAD1, GAD2, MEIS2
IGFBP5, CHRM2, OTX2, DMBX1, SV2C, NYAP2, DSEL, AC007159.1, NR2F2, DIRC3
AC110597.1, SLC32A1, GATA3, GREM2, PLCB1, ZFPM2, TSPAN18, CCSER1, IGSF21, CNTNAP2
Negative: GAP43, ELAVL4, NEFL, MAP1B, GLRA2, RND3, NEFM, GPRIN3, GABRG2, ELAVL2
TCF4, POU3F2, RAB3B, SCG2, TENM2, ARHGAP21, TMSB4X, PLPPR1, NOVA1, CRABP1
NTRK3, PIK3R1, DNAJC6, SLC17A6, ANKS1B, TENM1, DACH1, SYT4, FGF12, PCDH17 PCAPlot(con_seu_ft)
#Assess how many PCs capture most of the information in the data
ElbowPlot(con_seu_ft, ndims = 30)
We won’t run this code I’ve included this analysis that calculates the cut-off for signicance of component numbers. However the function runs multiple iterations of the PCA and will take a long time to run.
# Jackstraw
#Assess how many PCs capture most of the information in the data
seu <-JackStraw(seu, reduction = "pca",
dims = 30)
seu <- ScoreJackStraw(seu, reduction = "pca", dims = 1:30)
JackStrawPlot(seu, dims = 1:30)
Non-linear dimensional reduction using UMAP
#Non-linear dimensionality reduction
#Choosing how many PCs to input can depend on the elbow plot and on the number of cells
#There are many parameters that can e tweaked and optimized in a UMAP plot
#You can see some demos here: https://pair-code.github.io/understanding-umap/
con_seu_ft <- RunUMAP(con_seu_ft, dims = 1:18)Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
14:31:52 UMAP embedding parameters a = 0.9922 b = 1.112
14:31:52 Read 2938 rows and found 18 numeric columns
14:31:52 Using Annoy for neighbor search, n_neighbors = 30
14:31:52 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:31:53 Writing NN index file to temp file /var/folders/k4/khtkczkd5tn732ftjpwgtr240000gn/T//RtmpgyVOQf/fileaa4e718c5243
14:31:53 Searching Annoy index using 1 thread, search_k = 3000
14:31:53 Annoy recall = 100%
14:31:54 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
14:31:55 Initializing from normalized Laplacian + noise (using irlba)
14:31:55 Commencing optimization for 500 epochs, with 116704 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
14:32:00 Optimization finishedUMAPPlot(con_seu_ft)
NA
NADoublet identification
# Assess possible doublets -----------------------------------------------
#Using instructions here: https://github.com/chris-mcginnis-ucsf/
#First we have to find a pK which determines how big of a neighborhood will be examined for doublets
#This should be chosen for each library separately
#First we test a number of pN (proportion of generated artificial doublets) and pK
#We get different lists of probabilities of artifical nearest neighbors with these tested parameters
#Also keep in mind the results are not deterministic (every run will give slightly different results)
sweep.res.con <- paramSweep_v3(con_seu_ft, PCs = 1:18, sct = FALSE)Loading required package: fields
Loading required package: spam
Spam version 2.9-1 (2022-08-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: ‘spam’
The following object is masked from ‘package:Matrix’:
det
The following object is masked from ‘package:stats4’:
mle
The following objects are masked from ‘package:base’:
backsolve, forwardsolve
Loading required package: viridis
Loading required package: viridisLite
Try help(fields) to get started.[1] "Creating artificial doublets for pN = 5%"
[1] "Creating Seurat object..."
[1] "Normalizing Seurat object..."Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Finding variable genes..."Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Scaling data..."Centering and scaling data matrix
|
| | 0%
|
|===================================== | 50%
|
|==========================================================================| 100%[1] "Running PCA..."
[1] "Calculating PC distance matrix..."
[1] "Defining neighborhoods..."
[1] "Computing pANN across all pK..."
[1] "pK = 0.005..."
[1] "pK = 0.01..."
[1] "pK = 0.02..."
[1] "pK = 0.03..."
[1] "pK = 0.04..."
[1] "pK = 0.05..."
[1] "pK = 0.06..."
[1] "pK = 0.07..."
[1] "pK = 0.08..."
[1] "pK = 0.09..."
[1] "pK = 0.1..."
[1] "pK = 0.11..."
[1] "pK = 0.12..."
[1] "pK = 0.13..."
[1] "pK = 0.14..."
[1] "pK = 0.15..."
[1] "pK = 0.16..."
[1] "pK = 0.17..."
[1] "pK = 0.18..."
[1] "pK = 0.19..."
[1] "pK = 0.2..."
[1] "pK = 0.21..."
[1] "pK = 0.22..."
[1] "pK = 0.23..."
[1] "pK = 0.24..."
[1] "pK = 0.25..."
[1] "pK = 0.26..."
[1] "pK = 0.27..."
[1] "pK = 0.28..."
[1] "pK = 0.29..."
[1] "pK = 0.3..."
[1] "Creating artificial doublets for pN = 10%"
[1] "Creating Seurat object..."
[1] "Normalizing Seurat object..."Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Finding variable genes..."Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Scaling data..."Centering and scaling data matrix
|
| | 0%
|
|===================================== | 50%
|
|==========================================================================| 100%[1] "Running PCA..."
[1] "Calculating PC distance matrix..."
[1] "Defining neighborhoods..."
[1] "Computing pANN across all pK..."
[1] "pK = 0.005..."
[1] "pK = 0.01..."
[1] "pK = 0.02..."
[1] "pK = 0.03..."
[1] "pK = 0.04..."
[1] "pK = 0.05..."
[1] "pK = 0.06..."
[1] "pK = 0.07..."
[1] "pK = 0.08..."
[1] "pK = 0.09..."
[1] "pK = 0.1..."
[1] "pK = 0.11..."
[1] "pK = 0.12..."
[1] "pK = 0.13..."
[1] "pK = 0.14..."
[1] "pK = 0.15..."
[1] "pK = 0.16..."
[1] "pK = 0.17..."
[1] "pK = 0.18..."
[1] "pK = 0.19..."
[1] "pK = 0.2..."
[1] "pK = 0.21..."
[1] "pK = 0.22..."
[1] "pK = 0.23..."
[1] "pK = 0.24..."
[1] "pK = 0.25..."
[1] "pK = 0.26..."
[1] "pK = 0.27..."
[1] "pK = 0.28..."
[1] "pK = 0.29..."
[1] "pK = 0.3..."
[1] "Creating artificial doublets for pN = 15%"
[1] "Creating Seurat object..."
[1] "Normalizing Seurat object..."Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Finding variable genes..."Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Scaling data..."Centering and scaling data matrix
|
| | 0%
|
|===================================== | 50%
|
|==========================================================================| 100%[1] "Running PCA..."
[1] "Calculating PC distance matrix..."
[1] "Defining neighborhoods..."
[1] "Computing pANN across all pK..."
[1] "pK = 0.005..."
[1] "pK = 0.01..."
[1] "pK = 0.02..."
[1] "pK = 0.03..."
[1] "pK = 0.04..."
[1] "pK = 0.05..."
[1] "pK = 0.06..."
[1] "pK = 0.07..."
[1] "pK = 0.08..."
[1] "pK = 0.09..."
[1] "pK = 0.1..."
[1] "pK = 0.11..."
[1] "pK = 0.12..."
[1] "pK = 0.13..."
[1] "pK = 0.14..."
[1] "pK = 0.15..."
[1] "pK = 0.16..."
[1] "pK = 0.17..."
[1] "pK = 0.18..."
[1] "pK = 0.19..."
[1] "pK = 0.2..."
[1] "pK = 0.21..."
[1] "pK = 0.22..."
[1] "pK = 0.23..."
[1] "pK = 0.24..."
[1] "pK = 0.25..."
[1] "pK = 0.26..."
[1] "pK = 0.27..."
[1] "pK = 0.28..."
[1] "pK = 0.29..."
[1] "pK = 0.3..."
[1] "Creating artificial doublets for pN = 20%"
[1] "Creating Seurat object..."
[1] "Normalizing Seurat object..."Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Finding variable genes..."Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Scaling data..."Centering and scaling data matrix
|
| | 0%
|
|===================================== | 50%
|
|==========================================================================| 100%[1] "Running PCA..."
[1] "Calculating PC distance matrix..."
[1] "Defining neighborhoods..."
[1] "Computing pANN across all pK..."
[1] "pK = 0.005..."
[1] "pK = 0.01..."
[1] "pK = 0.02..."
[1] "pK = 0.03..."
[1] "pK = 0.04..."
[1] "pK = 0.05..."
[1] "pK = 0.06..."
[1] "pK = 0.07..."
[1] "pK = 0.08..."
[1] "pK = 0.09..."
[1] "pK = 0.1..."
[1] "pK = 0.11..."
[1] "pK = 0.12..."
[1] "pK = 0.13..."
[1] "pK = 0.14..."
[1] "pK = 0.15..."
[1] "pK = 0.16..."
[1] "pK = 0.17..."
[1] "pK = 0.18..."
[1] "pK = 0.19..."
[1] "pK = 0.2..."
[1] "pK = 0.21..."
[1] "pK = 0.22..."
[1] "pK = 0.23..."
[1] "pK = 0.24..."
[1] "pK = 0.25..."
[1] "pK = 0.26..."
[1] "pK = 0.27..."
[1] "pK = 0.28..."
[1] "pK = 0.29..."
[1] "pK = 0.3..."
[1] "Creating artificial doublets for pN = 25%"
[1] "Creating Seurat object..."
[1] "Normalizing Seurat object..."Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Finding variable genes..."Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Scaling data..."Centering and scaling data matrix
|
| | 0%
|
|===================================== | 50%
|
|==========================================================================| 100%[1] "Running PCA..."
[1] "Calculating PC distance matrix..."
[1] "Defining neighborhoods..."
[1] "Computing pANN across all pK..."
[1] "pK = 0.005..."
[1] "pK = 0.01..."
[1] "pK = 0.02..."
[1] "pK = 0.03..."
[1] "pK = 0.04..."
[1] "pK = 0.05..."
[1] "pK = 0.06..."
[1] "pK = 0.07..."
[1] "pK = 0.08..."
[1] "pK = 0.09..."
[1] "pK = 0.1..."
[1] "pK = 0.11..."
[1] "pK = 0.12..."
[1] "pK = 0.13..."
[1] "pK = 0.14..."
[1] "pK = 0.15..."
[1] "pK = 0.16..."
[1] "pK = 0.17..."
[1] "pK = 0.18..."
[1] "pK = 0.19..."
[1] "pK = 0.2..."
[1] "pK = 0.21..."
[1] "pK = 0.22..."
[1] "pK = 0.23..."
[1] "pK = 0.24..."
[1] "pK = 0.25..."
[1] "pK = 0.26..."
[1] "pK = 0.27..."
[1] "pK = 0.28..."
[1] "pK = 0.29..."
[1] "pK = 0.3..."
[1] "Creating artificial doublets for pN = 30%"
[1] "Creating Seurat object..."
[1] "Normalizing Seurat object..."Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Finding variable genes..."Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Scaling data..."Centering and scaling data matrix
|
| | 0%
|
|===================================== | 50%
|
|==========================================================================| 100%[1] "Running PCA..."
[1] "Calculating PC distance matrix..."
[1] "Defining neighborhoods..."
[1] "Computing pANN across all pK..."
[1] "pK = 0.005..."
[1] "pK = 0.01..."
[1] "pK = 0.02..."
[1] "pK = 0.03..."
[1] "pK = 0.04..."
[1] "pK = 0.05..."
[1] "pK = 0.06..."
[1] "pK = 0.07..."
[1] "pK = 0.08..."
[1] "pK = 0.09..."
[1] "pK = 0.1..."
[1] "pK = 0.11..."
[1] "pK = 0.12..."
[1] "pK = 0.13..."
[1] "pK = 0.14..."
[1] "pK = 0.15..."
[1] "pK = 0.16..."
[1] "pK = 0.17..."
[1] "pK = 0.18..."
[1] "pK = 0.19..."
[1] "pK = 0.2..."
[1] "pK = 0.21..."
[1] "pK = 0.22..."
[1] "pK = 0.23..."
[1] "pK = 0.24..."
[1] "pK = 0.25..."
[1] "pK = 0.26..."
[1] "pK = 0.27..."
[1] "pK = 0.28..."
[1] "pK = 0.29..."
[1] "pK = 0.3..."#We do not have the "ground truth" regarding doublets, such from from genotype data for pooled samples
#We sumamrize the performance of the range of pN=pK parameters we tested
sweep.stats_con <- summarizeSweep(sweep.res.con, GT = FALSE)Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: ROCR#Here the "best" pK for the data is chosen based on a metric determined by the DoubletFinder developers
#Which performs best in datasets where the ground truth is known
bcmvn_con <- find.pK(sweep.stats_con)NULL
ggplot(bcmvn_con, aes(x = pK, y = BCmetric, group = "Sweep")) + geom_point() + geom_line() +
theme(axis.text.x = element_text(angle = 90))
#We will pick pK = 0.08
#We are not going to use our clustering information to estimate "homotypic" doublets
#We are simply going to use an expected doublet formation rate of 2.5% based on the number of starting cells loaded
nExp_poi <- round(0.025*nrow(con_seu_ft@meta.data))
con_seu_ft <- doubletFinder_v3(con_seu_ft, PCs = 1:18, pN = 0.25, pK = 0.08, nExp = nExp_poi, reuse.pANN = FALSE, sct = FALSE)[1] "Creating 979 artificial doublets..."
[1] "Creating Seurat object..."
[1] "Normalizing Seurat object..."Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Finding variable genes..."Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|[1] "Scaling data..."Centering and scaling data matrix
|
| | 0%
|
|===================================== | 50%
|
|==========================================================================| 100%[1] "Running PCA..."
[1] "Calculating PC distance matrix..."
[1] "Computing pANN..."
[1] "Classifying doublets.."#Here we update the Seurat object version just in case the one returned by DoubletFinder is an older version
con_seu_ft <- UpdateSeuratObject(con_seu_ft)Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Object representation is consistent with the most current Seurat version# we have now identified doublets but we have not removed them
Visualize the doublet removal results
# we need to look in the data object
#Visualize and assess the cells called as probable doublets
UMAPPlot(con_seu_ft, group.by = "DF.classifications_0.25_0.08_73")
# table of doublets and signlets
con_seu_ft$DF.classifications_0.25_0.08_73 %>% table.
Doublet Singlet
73 2865 # visualize the features in doublets and singlets
VlnPlot(con_seu_ft, features = c("nCount_RNA", "nFeature_RNA", "percent.MT", "pANN_0.25_0.08_73"),
group.by = "DF.classifications_0.25_0.08_73", pt.size = 0.001, ncol = 2, log = TRUE)
# remove the doublets
# we can do this by subset
# first we need to set the active meta data slot to the doublet identification
Idents(con_seu_ft) <- "DF.classifications_0.25_0.08_73"
# we select only the singlet cells
con_seu_ft2 <- subset(con_seu_ft, idents = "Singlet")
dim(con_seu_ft)[1] 18557 2938dim(con_seu_ft2)[1] 18557 2865Repeat the above steps for the SNCA triplication patient line
# read in data
ast_data <- Read10X("/Users/rhalenathomas/Documents/Data/scRNAseq/AST23_BrainComm/CellRangerOuts/AST23/raw_feature_bc_matrix")
# create seurat object
# filter object with the same settings as with the control
# PCA analysis
# Remove doublets
# clean up
rm(ast_data,ast_seu_ft,bcmvn_ast,bcmvn_con,con_seu_ft, sweep.res.ast, sweep.res.con, sweep.stats_ast, sweep.stats_con)BREAK
Merge data objects
merge_seurat <- merge(con_seu_ft2,ast_seu_ft2)Warning in CheckDuplicateCellNames(object.list = objects) :
Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.merge_seuratAn object of class Seurat
19204 features across 4028 samples within 1 assay
Active assay: RNA (19204 features, 0 variable features)unique(merge_seurat$orig.ident)[1] "Control" "SNCA" Find anchors between the two data objects
sample.list <- SplitObject(merge_seurat, split.by = "orig.ident")
# We have already normalized and identified variable features in each sample
# If we had not done so we can normalize here
#for (i in 1:length(sample.list)){
# org.list[[i]] <- NormalizeData(org.list[[i]], verbose = FALSE)
#org.list[[i]] <- FindVariableFeatures(org.list[[i]], selection.method = "vst")
#}
# Now we find features that can act as anchors between the two samples
int.anchors <- FindIntegrationAnchors(object.list = sample.list, dims = 1:50)Computing 2000 integration features
No variable features found for object1 in the object.list. Running FindVariableFeatures ...
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
No variable features found for object2 in the object.list. Running FindVariableFeatures ...
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Scaling features for provided objects
| | 0 % ~calculating
|+++++++++++++++++++++++++ | 50% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s Finding all pairwise anchors
| | 0 % ~calculating Running CCA
Merging objects
Finding neighborhoods
Finding anchors
Found 4320 anchors
Filtering anchors
Retained 3529 anchors
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=16s integrated_seurat <- IntegrateData(anchorset = int.anchors, dims = 1:50)Merging dataset 2 into 1
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating dataOptional: save the integrated object or read in the Integrated object for the next step.
# remove # comment from the code you want to run
saveRDS(integrated_seurat,"IntegratedSeurat.RDS")
#integrated_seurate <- readRDS("IntegratedSeurat.RDS")
PCA and UMAP on the merged object
# merged object
DefaultAssay(merge_seurat) <- "RNA"
merge_seurat <- ScaleData(merge_seurat, verbose = FALSE)
# in the merge data set we sill need features for the PCA input
merge_seurat <- FindVariableFeatures(merge_seurat, selection.method = "vst")Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|merge_seurat <- RunPCA(merge_seurat, npcs = 30, verbose = FALSE)
merge_seurat <- RunUMAP(merge_seurat, reduction = "pca", dims = 1:30)15:10:21 UMAP embedding parameters a = 0.9922 b = 1.112
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
15:10:21 Read 4028 rows and found 30 numeric columns
15:10:21 Using Annoy for neighbor search, n_neighbors = 30
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
15:10:21 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
15:10:22 Writing NN index file to temp file /var/folders/k4/khtkczkd5tn732ftjpwgtr240000gn/T//RtmpgyVOQf/fileaa4ec70e42c
15:10:22 Searching Annoy index using 1 thread, search_k = 3000
15:10:22 Annoy recall = 100%
15:10:23 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
15:10:24 Initializing from normalized Laplacian + noise (using irlba)
15:10:24 Commencing optimization for 500 epochs, with 163142 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
15:10:31 Optimization finishedRepeat PCA and UMAP for the integrated object
Idents(integrated_seurat) <- "integrated"
integrated_seurat <- ScaleData(integrated_seurat, verbose = FALSE)
# only the integrated features will be the pca input
integrated_seurat <- RunPCA(integrated_seurat, npcs = 30, verbose = FALSE)
integrated_seurat <- RunUMAP(integrated_seurat, reduction = "pca", dims = 1:30)15:10:48 UMAP embedding parameters a = 0.9922 b = 1.112
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
15:10:48 Read 4028 rows and found 30 numeric columns
15:10:48 Using Annoy for neighbor search, n_neighbors = 30
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
15:10:48 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
15:10:48 Writing NN index file to temp file /var/folders/k4/khtkczkd5tn732ftjpwgtr240000gn/T//RtmpgyVOQf/fileaa4e47940b15
15:10:48 Searching Annoy index using 1 thread, search_k = 3000
15:10:49 Annoy recall = 100%
15:10:49 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
15:10:50 Initializing from normalized Laplacian + noise (using irlba)
15:10:50 Commencing optimization for 500 epochs, with 165954 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
15:10:57 Optimization finishedOptional: save the PCA and UMAP integrated object or read in the saved object
# remove # comment from the code you want to run
saveRDS(integrated_seurat,"IntegratedSeuratGraphs.RDS")
#integrated_seurat <- readRDS("IntegratedSeuratGraphs.RDS")
Let’s look at the UMAPs from the merged vs the integrated data
p1 <- DimPlot(merge_seurat, group.by = "orig.ident") + ggtitle("Merge")p2 <- DimPlot(integrated_seurat, group.by = "orig.ident") + ggtitle("Integrated")
p1
p2
We see almost no difference in this data. This is not the case in all data sets
Cluster the integrated data
# see the importance of the pca components
ElbowPlot(integrated_seurat, ndims=30)
integrated_seuratAn object of class Seurat
21204 features across 4028 samples within 2 assays
Active assay: integrated (2000 features, 2000 variable features)
1 other assay present: RNA
2 dimensional reductions calculated: pca, umapdim(integrated_seurat)[1] 2000 4028We will choose 20 PCs There are 4028 cells. A common rule of thumb for choosing k for nearest neighbours is using the square root of the number of cells = 63
Visualize the UMAP of the different cluster resolutions
res <- c(0.05,0.25,0.4,0.5,0.6,1,1.5)
resolutions <- paste("integrated_snn_res.", res, sep="")
resolutions[1] "integrated_snn_res.0.05" "integrated_snn_res.0.25" "integrated_snn_res.0.4"
[4] "integrated_snn_res.0.5" "integrated_snn_res.0.6" "integrated_snn_res.1"
[7] "integrated_snn_res.1.5" for(r in resolutions){
print(DimPlot(integrated_seurat, group.by = r))
}
NA
NABREAK
Now we need to choose a resolution to annotate. I will select resolution of 0.6.
# Scale the total RNA
# before we only scaled the integrated expression for the genes used for integration
# now we want to scale all genes
DefaultAssay(integrated_seurat) <- "RNA"
integrated_seurat <- ScaleData(integrated_seurat)Centering and scaling data matrix
|
| | 0%
|
|==== | 5%
|
|======== | 10%
|
|============= | 15%
|
|================= | 20%
|
|===================== | 25%
|
|========================= | 30%
|
|============================= | 35%
|
|================================== | 40%
|
|====================================== | 45%
|
|========================================== | 50%
|
|============================================== | 55%
|
|================================================== | 60%
|
|======================================================= | 65%
|
|=========================================================== | 70%
|
|=============================================================== | 75%
|
|=================================================================== | 80%
|
|======================================================================= | 85%
|
|============================================================================ | 90%
|
|================================================================================ | 95%
|
|====================================================================================| 100%Look at known cell type markers
# features list from literature
da_neurons <- c("TH","SLC6A3","SLC18A2","SOX6","NDNF","SNCG","ALDH1A1","CALB1","TACR2","SLC17A6","SLC32A1","OTX2","GRP","LPL","CCK","VIP")
NPC_orStemLike <- c("DCX","NEUROD1","TBR1","PCNA","MKI67","SOX2","NES","PAX6","MASH1")
mature_neurons = c("RBFOX3","SYP","DLG45","VAMP1","VAMP2","TUBB3","SYT1","BSN","HOMER1","SLC17A6")
excitatory_neurons = c("GRIA2","GRIA1","GRIA4","GRIN1","GRIN2B","GRIN2A","GRIN3A","GRIN3","GRIP1","CAMK2A")
inhbitory_neurons = inh = c("GAD1","GAD2", "GAT1","PVALB","GABR2","GABR1","GBRR1","GABRB2","GABRB1","GABRB3","GABRA6","GABRA1","GABRA4","TRAK2")
astrocytes <- c("GFAP","S100B","AQP4","APOE", "SOX9","SLC1A3")
oligodendrocytes <- c("MBP","MOG","OLIG1","OLIG2","SOX10")
opc <-
radial_glia <- c("PTPRC","AIF1","ADGRE1", "VIM", "TNC","PTPRZ1","FAM107A","HOPX","LIFR",
"ITGB5","IL6ST","SLC1A3")
epithelial <- c("HES1","HES5","SOX2","SOX10","NES","CDH1","NOTCH1")
microglia <- c("IBA1","P2RY12","P2RY13","TREM119", "GPR34","SIGLECH","TREM2",
"CX3CR1","FCRLS","OLFML3","HEXB","TGFBR1", "SALL1","MERTK",
"PROS1")
features_list <- c("MKI67","SOX2","POU5F1","DLX2","PAX6","SOX9","HES1","NES","RBFOX3","MAP2","NCAM1","CD24","GRIA2","GRIN2B","GABBR1","GAD1","GAD2","GABRA1","GABRB2","TH","ALDH1A1","LMX1B","NR4A2","CORIN","CALB1","KCNJ6","CXCR4","ITGA6","SLC1A3","CD44","AQP4","S100B", "PDGFRA","OLIG2","MBP","CLDN11","VIM","VCAM1")
short_list <- c("MKI67","SOX9","HES1","NES","DLX2","RBFOX3","MAP2","TH","CALB1","KCNJ6","SLC1A3","CD44","AQP4","S100B","OLIG2","MBP","VIM")
Seurat has several helpful plotting function that use ggplot
# we set the active identity of the meta data to be the clusters at the resolution we want to label
Idents(integrated_seurat) <- "integrated_snn_res.0.6"
FeaturePlot(integrated_seurat, label = TRUE, features = short_list)
NA
NA
NA# this will let us see one at at time
for (i in short_list) {
print(FeaturePlot(integrated_seurat, features = i, min.cutoff = 'q1', max.cutoff = 'q97', label = TRUE))
}
NA
NANow that we see the TH is all in one spot that is part of a large cluster we look back at the different cluster level.
Dot Plots
DotPlot(integrated_seurat, group.by = "integrated_snn_res.1",
features = short_list, assay = "RNA") + RotatedAxis()
DotPlot(integrated_seurat, group.by = "integrated_snn_res.1",
features = da_neurons, assay = "RNA") + RotatedAxis()Warning in FetchData.Seurat(object = object, vars = features, cells = cells) :
The following requested variables were not found: SLC6A3, TACR2, VIP
DotPlot(integrated_seurat, group.by = "integrated_snn_res.1",
features = mature_neurons, assay = "RNA") + RotatedAxis()Warning in FetchData.Seurat(object = object, vars = features, cells = cells) :
The following requested variables were not found: DLG45
Heatmaps
DoHeatmap(integrated_seurat, group.by = "integrated_snn_res.1",
features = short_list, slot = "scale.data")
NA
NALook at more expression lists
Find Cluster markers
# cluster markers will be calculated for the active identity
Idents(integrated_seurat) <- "integrated_snn_res.1"
ClusterMarkers <- FindAllMarkers(integrated_seurat, only.pos = TRUE)Calculating cluster 0
| | 0 % ~calculating
|+ | 1 % ~14s
|++ | 2 % ~14s
|++ | 3 % ~14s
|+++ | 4 % ~14s
|+++ | 5 % ~13s
|++++ | 6 % ~13s
|++++ | 8 % ~13s
|+++++ | 9 % ~13s
|+++++ | 10% ~13s
|++++++ | 11% ~12s
|++++++ | 12% ~12s
|+++++++ | 13% ~12s
|+++++++ | 14% ~12s
|++++++++ | 15% ~12s
|+++++++++ | 16% ~11s
|+++++++++ | 17% ~11s
|++++++++++ | 18% ~11s
|++++++++++ | 19% ~11s
|+++++++++++ | 20% ~11s
|+++++++++++ | 22% ~11s
|++++++++++++ | 23% ~10s
|++++++++++++ | 24% ~10s
|+++++++++++++ | 25% ~10s
|+++++++++++++ | 26% ~10s
|++++++++++++++ | 27% ~10s
|++++++++++++++ | 28% ~10s
|+++++++++++++++ | 29% ~10s
|++++++++++++++++ | 30% ~09s
|++++++++++++++++ | 31% ~09s
|+++++++++++++++++ | 32% ~09s
|+++++++++++++++++ | 33% ~09s
|++++++++++++++++++ | 34% ~09s
|++++++++++++++++++ | 35% ~09s
|+++++++++++++++++++ | 37% ~09s
|+++++++++++++++++++ | 38% ~09s
|++++++++++++++++++++ | 39% ~09s
|++++++++++++++++++++ | 40% ~08s
|+++++++++++++++++++++ | 41% ~08s
|+++++++++++++++++++++ | 42% ~08s
|++++++++++++++++++++++ | 43% ~08s
|+++++++++++++++++++++++ | 44% ~08s
|+++++++++++++++++++++++ | 45% ~08s
|++++++++++++++++++++++++ | 46% ~07s
|++++++++++++++++++++++++ | 47% ~07s
|+++++++++++++++++++++++++ | 48% ~07s
|+++++++++++++++++++++++++ | 49% ~07s
|++++++++++++++++++++++++++ | 51% ~07s
|++++++++++++++++++++++++++ | 52% ~07s
|+++++++++++++++++++++++++++ | 53% ~07s
|+++++++++++++++++++++++++++ | 54% ~06s
|++++++++++++++++++++++++++++ | 55% ~06s
|++++++++++++++++++++++++++++ | 56% ~06s
|+++++++++++++++++++++++++++++ | 57% ~06s
|++++++++++++++++++++++++++++++ | 58% ~06s
|++++++++++++++++++++++++++++++ | 59% ~06s
|+++++++++++++++++++++++++++++++ | 60% ~05s
|+++++++++++++++++++++++++++++++ | 61% ~05s
|++++++++++++++++++++++++++++++++ | 62% ~05s
|++++++++++++++++++++++++++++++++ | 63% ~05s
|+++++++++++++++++++++++++++++++++ | 65% ~05s
|+++++++++++++++++++++++++++++++++ | 66% ~05s
|++++++++++++++++++++++++++++++++++ | 67% ~05s
|++++++++++++++++++++++++++++++++++ | 68% ~04s
|+++++++++++++++++++++++++++++++++++ | 69% ~04s
|+++++++++++++++++++++++++++++++++++ | 70% ~04s
|++++++++++++++++++++++++++++++++++++ | 71% ~04s
|+++++++++++++++++++++++++++++++++++++ | 72% ~04s
|+++++++++++++++++++++++++++++++++++++ | 73% ~04s
|++++++++++++++++++++++++++++++++++++++ | 74% ~03s
|++++++++++++++++++++++++++++++++++++++ | 75% ~03s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~03s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~03s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~03s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 88% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=13s Calculating cluster 1
| | 0 % ~calculating
|+ | 1 % ~12s
|++ | 2 % ~11s
|++ | 3 % ~11s
|+++ | 4 % ~11s
|+++ | 5 % ~11s
|++++ | 7 % ~10s
|++++ | 8 % ~10s
|+++++ | 9 % ~10s
|+++++ | 10% ~10s
|++++++ | 11% ~10s
|+++++++ | 12% ~10s
|+++++++ | 13% ~10s
|++++++++ | 14% ~09s
|++++++++ | 15% ~09s
|+++++++++ | 16% ~09s
|+++++++++ | 18% ~09s
|++++++++++ | 19% ~09s
|++++++++++ | 20% ~09s
|+++++++++++ | 21% ~09s
|+++++++++++ | 22% ~09s
|++++++++++++ | 23% ~08s
|+++++++++++++ | 24% ~08s
|+++++++++++++ | 25% ~08s
|++++++++++++++ | 26% ~08s
|++++++++++++++ | 27% ~08s
|+++++++++++++++ | 29% ~08s
|+++++++++++++++ | 30% ~08s
|++++++++++++++++ | 31% ~07s
|++++++++++++++++ | 32% ~07s
|+++++++++++++++++ | 33% ~07s
|++++++++++++++++++ | 34% ~07s
|++++++++++++++++++ | 35% ~07s
|+++++++++++++++++++ | 36% ~07s
|+++++++++++++++++++ | 37% ~07s
|++++++++++++++++++++ | 38% ~07s
|++++++++++++++++++++ | 40% ~07s
|+++++++++++++++++++++ | 41% ~06s
|+++++++++++++++++++++ | 42% ~06s
|++++++++++++++++++++++ | 43% ~06s
|++++++++++++++++++++++ | 44% ~06s
|+++++++++++++++++++++++ | 45% ~06s
|++++++++++++++++++++++++ | 46% ~06s
|++++++++++++++++++++++++ | 47% ~06s
|+++++++++++++++++++++++++ | 48% ~06s
|+++++++++++++++++++++++++ | 49% ~05s
|++++++++++++++++++++++++++ | 51% ~05s
|++++++++++++++++++++++++++ | 52% ~05s
|+++++++++++++++++++++++++++ | 53% ~05s
|+++++++++++++++++++++++++++ | 54% ~05s
|++++++++++++++++++++++++++++ | 55% ~05s
|+++++++++++++++++++++++++++++ | 56% ~05s
|+++++++++++++++++++++++++++++ | 57% ~05s
|++++++++++++++++++++++++++++++ | 58% ~04s
|++++++++++++++++++++++++++++++ | 59% ~04s
|+++++++++++++++++++++++++++++++ | 60% ~04s
|+++++++++++++++++++++++++++++++ | 62% ~04s
|++++++++++++++++++++++++++++++++ | 63% ~04s
|++++++++++++++++++++++++++++++++ | 64% ~04s
|+++++++++++++++++++++++++++++++++ | 65% ~04s
|+++++++++++++++++++++++++++++++++ | 66% ~04s
|++++++++++++++++++++++++++++++++++ | 67% ~04s
|+++++++++++++++++++++++++++++++++++ | 68% ~03s
|+++++++++++++++++++++++++++++++++++ | 69% ~03s
|++++++++++++++++++++++++++++++++++++ | 70% ~03s
|++++++++++++++++++++++++++++++++++++ | 71% ~03s
|+++++++++++++++++++++++++++++++++++++ | 73% ~03s
|+++++++++++++++++++++++++++++++++++++ | 74% ~03s
|++++++++++++++++++++++++++++++++++++++ | 75% ~03s
|++++++++++++++++++++++++++++++++++++++ | 76% ~03s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=11s Calculating cluster 2
| | 0 % ~calculating
|+ | 1 % ~07s
|+ | 2 % ~07s
|++ | 3 % ~07s
|++ | 4 % ~07s
|+++ | 5 % ~06s
|+++ | 6 % ~06s
|++++ | 7 % ~06s
|++++ | 8 % ~06s
|+++++ | 9 % ~06s
|+++++ | 10% ~06s
|++++++ | 11% ~06s
|++++++ | 12% ~06s
|+++++++ | 13% ~06s
|+++++++ | 14% ~06s
|++++++++ | 15% ~06s
|++++++++ | 16% ~06s
|+++++++++ | 17% ~06s
|+++++++++ | 18% ~06s
|++++++++++ | 19% ~05s
|++++++++++ | 20% ~05s
|+++++++++++ | 21% ~05s
|+++++++++++ | 22% ~05s
|++++++++++++ | 23% ~05s
|++++++++++++ | 24% ~05s
|+++++++++++++ | 25% ~05s
|+++++++++++++ | 26% ~05s
|++++++++++++++ | 27% ~05s
|++++++++++++++ | 28% ~05s
|+++++++++++++++ | 29% ~05s
|+++++++++++++++ | 30% ~05s
|++++++++++++++++ | 31% ~05s
|++++++++++++++++ | 32% ~05s
|+++++++++++++++++ | 33% ~05s
|+++++++++++++++++ | 34% ~04s
|++++++++++++++++++ | 35% ~04s
|++++++++++++++++++ | 36% ~04s
|+++++++++++++++++++ | 37% ~04s
|+++++++++++++++++++ | 38% ~04s
|++++++++++++++++++++ | 39% ~04s
|++++++++++++++++++++ | 40% ~04s
|+++++++++++++++++++++ | 41% ~04s
|+++++++++++++++++++++ | 42% ~04s
|++++++++++++++++++++++ | 43% ~04s
|++++++++++++++++++++++ | 44% ~04s
|+++++++++++++++++++++++ | 45% ~04s
|+++++++++++++++++++++++ | 46% ~04s
|++++++++++++++++++++++++ | 47% ~04s
|++++++++++++++++++++++++ | 48% ~04s
|+++++++++++++++++++++++++ | 49% ~03s
|+++++++++++++++++++++++++ | 50% ~03s
|++++++++++++++++++++++++++ | 51% ~03s
|++++++++++++++++++++++++++ | 52% ~03s
|+++++++++++++++++++++++++++ | 53% ~03s
|+++++++++++++++++++++++++++ | 54% ~03s
|++++++++++++++++++++++++++++ | 55% ~03s
|++++++++++++++++++++++++++++ | 56% ~03s
|+++++++++++++++++++++++++++++ | 57% ~03s
|+++++++++++++++++++++++++++++ | 58% ~03s
|++++++++++++++++++++++++++++++ | 59% ~03s
|++++++++++++++++++++++++++++++ | 60% ~03s
|+++++++++++++++++++++++++++++++ | 61% ~03s
|+++++++++++++++++++++++++++++++ | 62% ~03s
|++++++++++++++++++++++++++++++++ | 63% ~03s
|++++++++++++++++++++++++++++++++ | 64% ~02s
|+++++++++++++++++++++++++++++++++ | 65% ~02s
|+++++++++++++++++++++++++++++++++ | 66% ~02s
|++++++++++++++++++++++++++++++++++ | 67% ~02s
|++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 69% ~02s
|+++++++++++++++++++++++++++++++++++ | 70% ~02s
|++++++++++++++++++++++++++++++++++++ | 71% ~02s
|++++++++++++++++++++++++++++++++++++ | 72% ~02s
|+++++++++++++++++++++++++++++++++++++ | 73% ~02s
|+++++++++++++++++++++++++++++++++++++ | 74% ~02s
|++++++++++++++++++++++++++++++++++++++ | 75% ~02s
|++++++++++++++++++++++++++++++++++++++ | 76% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=07s Calculating cluster 3
| | 0 % ~calculating
|+ | 1 % ~19s
|++ | 2 % ~19s
|++ | 3 % ~19s
|+++ | 4 % ~18s
|+++ | 5 % ~18s
|++++ | 6 % ~18s
|++++ | 7 % ~17s
|+++++ | 8 % ~17s
|+++++ | 9 % ~17s
|++++++ | 10% ~17s
|++++++ | 11% ~17s
|+++++++ | 12% ~16s
|+++++++ | 14% ~16s
|++++++++ | 15% ~16s
|++++++++ | 16% ~16s
|+++++++++ | 17% ~16s
|+++++++++ | 18% ~15s
|++++++++++ | 19% ~15s
|++++++++++ | 20% ~15s
|+++++++++++ | 21% ~15s
|+++++++++++ | 22% ~15s
|++++++++++++ | 23% ~14s
|++++++++++++ | 24% ~14s
|+++++++++++++ | 25% ~14s
|++++++++++++++ | 26% ~14s
|++++++++++++++ | 27% ~14s
|+++++++++++++++ | 28% ~13s
|+++++++++++++++ | 29% ~13s
|++++++++++++++++ | 30% ~13s
|++++++++++++++++ | 31% ~13s
|+++++++++++++++++ | 32% ~13s
|+++++++++++++++++ | 33% ~12s
|++++++++++++++++++ | 34% ~12s
|++++++++++++++++++ | 35% ~12s
|+++++++++++++++++++ | 36% ~12s
|+++++++++++++++++++ | 38% ~12s
|++++++++++++++++++++ | 39% ~11s
|++++++++++++++++++++ | 40% ~11s
|+++++++++++++++++++++ | 41% ~11s
|+++++++++++++++++++++ | 42% ~11s
|++++++++++++++++++++++ | 43% ~11s
|++++++++++++++++++++++ | 44% ~11s
|+++++++++++++++++++++++ | 45% ~10s
|+++++++++++++++++++++++ | 46% ~10s
|++++++++++++++++++++++++ | 47% ~10s
|++++++++++++++++++++++++ | 48% ~10s
|+++++++++++++++++++++++++ | 49% ~10s
|+++++++++++++++++++++++++ | 50% ~09s
|++++++++++++++++++++++++++ | 51% ~09s
|+++++++++++++++++++++++++++ | 52% ~09s
|+++++++++++++++++++++++++++ | 53% ~09s
|++++++++++++++++++++++++++++ | 54% ~09s
|++++++++++++++++++++++++++++ | 55% ~08s
|+++++++++++++++++++++++++++++ | 56% ~08s
|+++++++++++++++++++++++++++++ | 57% ~08s
|++++++++++++++++++++++++++++++ | 58% ~08s
|++++++++++++++++++++++++++++++ | 59% ~08s
|+++++++++++++++++++++++++++++++ | 60% ~07s
|+++++++++++++++++++++++++++++++ | 61% ~07s
|++++++++++++++++++++++++++++++++ | 62% ~07s
|++++++++++++++++++++++++++++++++ | 64% ~07s
|+++++++++++++++++++++++++++++++++ | 65% ~07s
|+++++++++++++++++++++++++++++++++ | 66% ~06s
|++++++++++++++++++++++++++++++++++ | 67% ~06s
|++++++++++++++++++++++++++++++++++ | 68% ~06s
|+++++++++++++++++++++++++++++++++++ | 69% ~06s
|+++++++++++++++++++++++++++++++++++ | 70% ~06s
|++++++++++++++++++++++++++++++++++++ | 71% ~05s
|++++++++++++++++++++++++++++++++++++ | 72% ~05s
|+++++++++++++++++++++++++++++++++++++ | 73% ~05s
|+++++++++++++++++++++++++++++++++++++ | 74% ~05s
|++++++++++++++++++++++++++++++++++++++ | 75% ~05s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~04s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~04s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~04s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~04s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~04s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~03s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~03s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~03s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~03s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~03s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~03s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=18s Calculating cluster 4
| | 0 % ~calculating
|+ | 1 % ~06s
|++ | 2 % ~06s
|++ | 3 % ~06s
|+++ | 4 % ~06s
|+++ | 5 % ~06s
|++++ | 6 % ~06s
|++++ | 7 % ~06s
|+++++ | 8 % ~06s
|+++++ | 9 % ~06s
|++++++ | 10% ~05s
|++++++ | 11% ~05s
|+++++++ | 12% ~05s
|+++++++ | 14% ~05s
|++++++++ | 15% ~05s
|++++++++ | 16% ~05s
|+++++++++ | 17% ~05s
|+++++++++ | 18% ~05s
|++++++++++ | 19% ~05s
|++++++++++ | 20% ~05s
|+++++++++++ | 21% ~05s
|+++++++++++ | 22% ~05s
|++++++++++++ | 23% ~05s
|++++++++++++ | 24% ~05s
|+++++++++++++ | 25% ~05s
|++++++++++++++ | 26% ~05s
|++++++++++++++ | 27% ~04s
|+++++++++++++++ | 28% ~04s
|+++++++++++++++ | 29% ~04s
|++++++++++++++++ | 30% ~04s
|++++++++++++++++ | 31% ~04s
|+++++++++++++++++ | 32% ~04s
|+++++++++++++++++ | 33% ~04s
|++++++++++++++++++ | 34% ~04s
|++++++++++++++++++ | 35% ~04s
|+++++++++++++++++++ | 36% ~04s
|+++++++++++++++++++ | 38% ~04s
|++++++++++++++++++++ | 39% ~04s
|++++++++++++++++++++ | 40% ~04s
|+++++++++++++++++++++ | 41% ~04s
|+++++++++++++++++++++ | 42% ~04s
|++++++++++++++++++++++ | 43% ~04s
|++++++++++++++++++++++ | 44% ~03s
|+++++++++++++++++++++++ | 45% ~03s
|+++++++++++++++++++++++ | 46% ~03s
|++++++++++++++++++++++++ | 47% ~03s
|++++++++++++++++++++++++ | 48% ~03s
|+++++++++++++++++++++++++ | 49% ~03s
|+++++++++++++++++++++++++ | 50% ~03s
|++++++++++++++++++++++++++ | 51% ~03s
|+++++++++++++++++++++++++++ | 52% ~03s
|+++++++++++++++++++++++++++ | 53% ~03s
|++++++++++++++++++++++++++++ | 54% ~03s
|++++++++++++++++++++++++++++ | 55% ~03s
|+++++++++++++++++++++++++++++ | 56% ~03s
|+++++++++++++++++++++++++++++ | 57% ~03s
|++++++++++++++++++++++++++++++ | 58% ~03s
|++++++++++++++++++++++++++++++ | 59% ~03s
|+++++++++++++++++++++++++++++++ | 60% ~02s
|+++++++++++++++++++++++++++++++ | 61% ~02s
|++++++++++++++++++++++++++++++++ | 62% ~02s
|++++++++++++++++++++++++++++++++ | 64% ~02s
|+++++++++++++++++++++++++++++++++ | 65% ~02s
|+++++++++++++++++++++++++++++++++ | 66% ~02s
|++++++++++++++++++++++++++++++++++ | 67% ~02s
|++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 69% ~02s
|+++++++++++++++++++++++++++++++++++ | 70% ~02s
|++++++++++++++++++++++++++++++++++++ | 71% ~02s
|++++++++++++++++++++++++++++++++++++ | 72% ~02s
|+++++++++++++++++++++++++++++++++++++ | 73% ~02s
|+++++++++++++++++++++++++++++++++++++ | 74% ~02s
|++++++++++++++++++++++++++++++++++++++ | 75% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06s Calculating cluster 5
| | 0 % ~calculating
|+ | 1 % ~15s
|++ | 2 % ~14s
|++ | 3 % ~13s
|+++ | 4 % ~13s
|+++ | 5 % ~13s
|++++ | 6 % ~13s
|++++ | 7 % ~13s
|+++++ | 8 % ~13s
|+++++ | 9 % ~13s
|++++++ | 10% ~12s
|++++++ | 11% ~12s
|+++++++ | 12% ~12s
|+++++++ | 13% ~12s
|++++++++ | 14% ~12s
|++++++++ | 15% ~12s
|+++++++++ | 16% ~12s
|+++++++++ | 17% ~12s
|++++++++++ | 18% ~11s
|++++++++++ | 19% ~12s
|+++++++++++ | 20% ~12s
|+++++++++++ | 21% ~12s
|++++++++++++ | 22% ~12s
|++++++++++++ | 23% ~11s
|+++++++++++++ | 24% ~11s
|+++++++++++++ | 26% ~11s
|++++++++++++++ | 27% ~11s
|++++++++++++++ | 28% ~11s
|+++++++++++++++ | 29% ~10s
|+++++++++++++++ | 30% ~10s
|++++++++++++++++ | 31% ~10s
|++++++++++++++++ | 32% ~10s
|+++++++++++++++++ | 33% ~10s
|+++++++++++++++++ | 34% ~10s
|++++++++++++++++++ | 35% ~10s
|++++++++++++++++++ | 36% ~09s
|+++++++++++++++++++ | 37% ~09s
|+++++++++++++++++++ | 38% ~09s
|++++++++++++++++++++ | 39% ~09s
|++++++++++++++++++++ | 40% ~09s
|+++++++++++++++++++++ | 41% ~09s
|+++++++++++++++++++++ | 42% ~08s
|++++++++++++++++++++++ | 43% ~08s
|++++++++++++++++++++++ | 44% ~08s
|+++++++++++++++++++++++ | 45% ~08s
|+++++++++++++++++++++++ | 46% ~08s
|++++++++++++++++++++++++ | 47% ~08s
|++++++++++++++++++++++++ | 48% ~07s
|+++++++++++++++++++++++++ | 49% ~07s
|+++++++++++++++++++++++++ | 50% ~07s
|++++++++++++++++++++++++++ | 51% ~07s
|+++++++++++++++++++++++++++ | 52% ~07s
|+++++++++++++++++++++++++++ | 53% ~07s
|++++++++++++++++++++++++++++ | 54% ~07s
|++++++++++++++++++++++++++++ | 55% ~06s
|+++++++++++++++++++++++++++++ | 56% ~06s
|+++++++++++++++++++++++++++++ | 57% ~06s
|++++++++++++++++++++++++++++++ | 58% ~06s
|++++++++++++++++++++++++++++++ | 59% ~06s
|+++++++++++++++++++++++++++++++ | 60% ~06s
|+++++++++++++++++++++++++++++++ | 61% ~06s
|++++++++++++++++++++++++++++++++ | 62% ~05s
|++++++++++++++++++++++++++++++++ | 63% ~05s
|+++++++++++++++++++++++++++++++++ | 64% ~05s
|+++++++++++++++++++++++++++++++++ | 65% ~05s
|++++++++++++++++++++++++++++++++++ | 66% ~05s
|++++++++++++++++++++++++++++++++++ | 67% ~05s
|+++++++++++++++++++++++++++++++++++ | 68% ~05s
|+++++++++++++++++++++++++++++++++++ | 69% ~04s
|++++++++++++++++++++++++++++++++++++ | 70% ~04s
|++++++++++++++++++++++++++++++++++++ | 71% ~04s
|+++++++++++++++++++++++++++++++++++++ | 72% ~04s
|+++++++++++++++++++++++++++++++++++++ | 73% ~04s
|++++++++++++++++++++++++++++++++++++++ | 74% ~04s
|++++++++++++++++++++++++++++++++++++++ | 76% ~03s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~03s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~03s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~03s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~03s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=14s Calculating cluster 6
| | 0 % ~calculating
|+ | 1 % ~20s
|++ | 2 % ~20s
|++ | 3 % ~20s
|+++ | 4 % ~20s
|+++ | 5 % ~19s
|++++ | 6 % ~19s
|++++ | 7 % ~19s
|+++++ | 8 % ~19s
|+++++ | 9 % ~19s
|++++++ | 10% ~19s
|++++++ | 11% ~18s
|+++++++ | 12% ~18s
|+++++++ | 13% ~18s
|++++++++ | 14% ~18s
|++++++++ | 15% ~18s
|+++++++++ | 16% ~17s
|+++++++++ | 18% ~17s
|++++++++++ | 19% ~17s
|++++++++++ | 20% ~17s
|+++++++++++ | 21% ~17s
|+++++++++++ | 22% ~16s
|++++++++++++ | 23% ~16s
|++++++++++++ | 24% ~16s
|+++++++++++++ | 25% ~16s
|+++++++++++++ | 26% ~15s
|++++++++++++++ | 27% ~15s
|++++++++++++++ | 28% ~15s
|+++++++++++++++ | 29% ~15s
|+++++++++++++++ | 30% ~15s
|++++++++++++++++ | 31% ~14s
|++++++++++++++++ | 32% ~14s
|+++++++++++++++++ | 33% ~14s
|++++++++++++++++++ | 34% ~14s
|++++++++++++++++++ | 35% ~13s
|+++++++++++++++++++ | 36% ~13s
|+++++++++++++++++++ | 37% ~13s
|++++++++++++++++++++ | 38% ~13s
|++++++++++++++++++++ | 39% ~13s
|+++++++++++++++++++++ | 40% ~12s
|+++++++++++++++++++++ | 41% ~12s
|++++++++++++++++++++++ | 42% ~12s
|++++++++++++++++++++++ | 43% ~12s
|+++++++++++++++++++++++ | 44% ~12s
|+++++++++++++++++++++++ | 45% ~11s
|++++++++++++++++++++++++ | 46% ~11s
|++++++++++++++++++++++++ | 47% ~11s
|+++++++++++++++++++++++++ | 48% ~11s
|+++++++++++++++++++++++++ | 49% ~11s
|++++++++++++++++++++++++++ | 51% ~10s
|++++++++++++++++++++++++++ | 52% ~10s
|+++++++++++++++++++++++++++ | 53% ~10s
|+++++++++++++++++++++++++++ | 54% ~10s
|++++++++++++++++++++++++++++ | 55% ~09s
|++++++++++++++++++++++++++++ | 56% ~09s
|+++++++++++++++++++++++++++++ | 57% ~09s
|+++++++++++++++++++++++++++++ | 58% ~09s
|++++++++++++++++++++++++++++++ | 59% ~09s
|++++++++++++++++++++++++++++++ | 60% ~08s
|+++++++++++++++++++++++++++++++ | 61% ~08s
|+++++++++++++++++++++++++++++++ | 62% ~08s
|++++++++++++++++++++++++++++++++ | 63% ~08s
|++++++++++++++++++++++++++++++++ | 64% ~07s
|+++++++++++++++++++++++++++++++++ | 65% ~07s
|+++++++++++++++++++++++++++++++++ | 66% ~07s
|++++++++++++++++++++++++++++++++++ | 67% ~07s
|+++++++++++++++++++++++++++++++++++ | 68% ~07s
|+++++++++++++++++++++++++++++++++++ | 69% ~06s
|++++++++++++++++++++++++++++++++++++ | 70% ~06s
|++++++++++++++++++++++++++++++++++++ | 71% ~06s
|+++++++++++++++++++++++++++++++++++++ | 72% ~06s
|+++++++++++++++++++++++++++++++++++++ | 73% ~06s
|++++++++++++++++++++++++++++++++++++++ | 74% ~05s
|++++++++++++++++++++++++++++++++++++++ | 75% ~05s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~05s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~05s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~05s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~04s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~04s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~04s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~04s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~03s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~03s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~03s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~03s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~03s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=21s Calculating cluster 7
| | 0 % ~calculating
|+ | 1 % ~12s
|++ | 2 % ~12s
|++ | 3 % ~12s
|+++ | 4 % ~12s
|+++ | 5 % ~11s
|++++ | 7 % ~11s
|++++ | 8 % ~11s
|+++++ | 9 % ~11s
|+++++ | 10% ~11s
|++++++ | 11% ~11s
|+++++++ | 12% ~10s
|+++++++ | 13% ~10s
|++++++++ | 14% ~10s
|++++++++ | 15% ~10s
|+++++++++ | 16% ~10s
|+++++++++ | 18% ~10s
|++++++++++ | 19% ~10s
|++++++++++ | 20% ~10s
|+++++++++++ | 21% ~10s
|+++++++++++ | 22% ~09s
|++++++++++++ | 23% ~09s
|+++++++++++++ | 24% ~09s
|+++++++++++++ | 25% ~09s
|++++++++++++++ | 26% ~09s
|++++++++++++++ | 27% ~09s
|+++++++++++++++ | 29% ~09s
|+++++++++++++++ | 30% ~09s
|++++++++++++++++ | 31% ~08s
|++++++++++++++++ | 32% ~08s
|+++++++++++++++++ | 33% ~08s
|++++++++++++++++++ | 34% ~08s
|++++++++++++++++++ | 35% ~08s
|+++++++++++++++++++ | 36% ~08s
|+++++++++++++++++++ | 37% ~08s
|++++++++++++++++++++ | 38% ~07s
|++++++++++++++++++++ | 40% ~07s
|+++++++++++++++++++++ | 41% ~07s
|+++++++++++++++++++++ | 42% ~07s
|++++++++++++++++++++++ | 43% ~07s
|++++++++++++++++++++++ | 44% ~07s
|+++++++++++++++++++++++ | 45% ~07s
|++++++++++++++++++++++++ | 46% ~07s
|++++++++++++++++++++++++ | 47% ~06s
|+++++++++++++++++++++++++ | 48% ~06s
|+++++++++++++++++++++++++ | 49% ~06s
|++++++++++++++++++++++++++ | 51% ~06s
|++++++++++++++++++++++++++ | 52% ~06s
|+++++++++++++++++++++++++++ | 53% ~06s
|+++++++++++++++++++++++++++ | 54% ~06s
|++++++++++++++++++++++++++++ | 55% ~05s
|+++++++++++++++++++++++++++++ | 56% ~05s
|+++++++++++++++++++++++++++++ | 57% ~05s
|++++++++++++++++++++++++++++++ | 58% ~05s
|++++++++++++++++++++++++++++++ | 59% ~05s
|+++++++++++++++++++++++++++++++ | 60% ~05s
|+++++++++++++++++++++++++++++++ | 62% ~05s
|++++++++++++++++++++++++++++++++ | 63% ~05s
|++++++++++++++++++++++++++++++++ | 64% ~04s
|+++++++++++++++++++++++++++++++++ | 65% ~04s
|+++++++++++++++++++++++++++++++++ | 66% ~04s
|++++++++++++++++++++++++++++++++++ | 67% ~04s
|+++++++++++++++++++++++++++++++++++ | 68% ~04s
|+++++++++++++++++++++++++++++++++++ | 69% ~04s
|++++++++++++++++++++++++++++++++++++ | 70% ~04s
|++++++++++++++++++++++++++++++++++++ | 71% ~04s
|+++++++++++++++++++++++++++++++++++++ | 73% ~03s
|+++++++++++++++++++++++++++++++++++++ | 74% ~03s
|++++++++++++++++++++++++++++++++++++++ | 75% ~03s
|++++++++++++++++++++++++++++++++++++++ | 76% ~03s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~03s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~03s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=12s Calculating cluster 8
| | 0 % ~calculating
|+ | 1 % ~10s
|++ | 2 % ~10s
|++ | 3 % ~10s
|+++ | 4 % ~10s
|+++ | 5 % ~09s
|++++ | 6 % ~09s
|++++ | 7 % ~09s
|+++++ | 9 % ~09s
|+++++ | 10% ~09s
|++++++ | 11% ~08s
|++++++ | 12% ~08s
|+++++++ | 13% ~08s
|+++++++ | 14% ~08s
|++++++++ | 15% ~08s
|++++++++ | 16% ~08s
|+++++++++ | 17% ~08s
|++++++++++ | 18% ~08s
|++++++++++ | 19% ~08s
|+++++++++++ | 20% ~07s
|+++++++++++ | 21% ~07s
|++++++++++++ | 22% ~07s
|++++++++++++ | 23% ~07s
|+++++++++++++ | 24% ~07s
|+++++++++++++ | 26% ~07s
|++++++++++++++ | 27% ~07s
|++++++++++++++ | 28% ~07s
|+++++++++++++++ | 29% ~07s
|+++++++++++++++ | 30% ~07s
|++++++++++++++++ | 31% ~06s
|++++++++++++++++ | 32% ~06s
|+++++++++++++++++ | 33% ~06s
|++++++++++++++++++ | 34% ~06s
|++++++++++++++++++ | 35% ~06s
|+++++++++++++++++++ | 36% ~06s
|+++++++++++++++++++ | 37% ~06s
|++++++++++++++++++++ | 38% ~06s
|++++++++++++++++++++ | 39% ~06s
|+++++++++++++++++++++ | 40% ~06s
|+++++++++++++++++++++ | 41% ~05s
|++++++++++++++++++++++ | 43% ~05s
|++++++++++++++++++++++ | 44% ~05s
|+++++++++++++++++++++++ | 45% ~05s
|+++++++++++++++++++++++ | 46% ~05s
|++++++++++++++++++++++++ | 47% ~05s
|++++++++++++++++++++++++ | 48% ~05s
|+++++++++++++++++++++++++ | 49% ~05s
|+++++++++++++++++++++++++ | 50% ~05s
|++++++++++++++++++++++++++ | 51% ~05s
|+++++++++++++++++++++++++++ | 52% ~04s
|+++++++++++++++++++++++++++ | 53% ~04s
|++++++++++++++++++++++++++++ | 54% ~04s
|++++++++++++++++++++++++++++ | 55% ~04s
|+++++++++++++++++++++++++++++ | 56% ~04s
|+++++++++++++++++++++++++++++ | 57% ~04s
|++++++++++++++++++++++++++++++ | 59% ~04s
|++++++++++++++++++++++++++++++ | 60% ~04s
|+++++++++++++++++++++++++++++++ | 61% ~04s
|+++++++++++++++++++++++++++++++ | 62% ~04s
|++++++++++++++++++++++++++++++++ | 63% ~03s
|++++++++++++++++++++++++++++++++ | 64% ~03s
|+++++++++++++++++++++++++++++++++ | 65% ~03s
|+++++++++++++++++++++++++++++++++ | 66% ~03s
|++++++++++++++++++++++++++++++++++ | 67% ~03s
|+++++++++++++++++++++++++++++++++++ | 68% ~03s
|+++++++++++++++++++++++++++++++++++ | 69% ~03s
|++++++++++++++++++++++++++++++++++++ | 70% ~03s
|++++++++++++++++++++++++++++++++++++ | 71% ~03s
|+++++++++++++++++++++++++++++++++++++ | 72% ~03s
|+++++++++++++++++++++++++++++++++++++ | 73% ~02s
|++++++++++++++++++++++++++++++++++++++ | 74% ~02s
|++++++++++++++++++++++++++++++++++++++ | 76% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=09s Calculating cluster 9
| | 0 % ~calculating
|+ | 1 % ~18s
|+ | 2 % ~17s
|++ | 3 % ~17s
|++ | 4 % ~16s
|+++ | 5 % ~16s
|+++ | 6 % ~16s
|++++ | 7 % ~16s
|++++ | 8 % ~15s
|+++++ | 9 % ~15s
|+++++ | 10% ~15s
|++++++ | 11% ~15s
|++++++ | 12% ~15s
|+++++++ | 13% ~15s
|+++++++ | 14% ~14s
|++++++++ | 15% ~14s
|++++++++ | 16% ~14s
|+++++++++ | 17% ~14s
|+++++++++ | 18% ~14s
|++++++++++ | 19% ~14s
|++++++++++ | 20% ~13s
|+++++++++++ | 21% ~13s
|+++++++++++ | 22% ~13s
|++++++++++++ | 23% ~13s
|++++++++++++ | 24% ~13s
|+++++++++++++ | 25% ~13s
|+++++++++++++ | 26% ~12s
|++++++++++++++ | 27% ~12s
|++++++++++++++ | 28% ~12s
|+++++++++++++++ | 29% ~12s
|+++++++++++++++ | 30% ~12s
|++++++++++++++++ | 31% ~12s
|++++++++++++++++ | 32% ~11s
|+++++++++++++++++ | 33% ~11s
|+++++++++++++++++ | 34% ~11s
|++++++++++++++++++ | 35% ~11s
|++++++++++++++++++ | 36% ~11s
|+++++++++++++++++++ | 37% ~11s
|+++++++++++++++++++ | 38% ~10s
|++++++++++++++++++++ | 39% ~10s
|++++++++++++++++++++ | 40% ~10s
|+++++++++++++++++++++ | 41% ~10s
|+++++++++++++++++++++ | 42% ~10s
|++++++++++++++++++++++ | 43% ~10s
|++++++++++++++++++++++ | 44% ~09s
|+++++++++++++++++++++++ | 45% ~09s
|+++++++++++++++++++++++ | 46% ~09s
|++++++++++++++++++++++++ | 47% ~09s
|++++++++++++++++++++++++ | 48% ~09s
|+++++++++++++++++++++++++ | 49% ~09s
|+++++++++++++++++++++++++ | 50% ~08s
|++++++++++++++++++++++++++ | 51% ~08s
|++++++++++++++++++++++++++ | 52% ~08s
|+++++++++++++++++++++++++++ | 53% ~08s
|+++++++++++++++++++++++++++ | 54% ~08s
|++++++++++++++++++++++++++++ | 55% ~08s
|++++++++++++++++++++++++++++ | 56% ~07s
|+++++++++++++++++++++++++++++ | 57% ~07s
|+++++++++++++++++++++++++++++ | 58% ~07s
|++++++++++++++++++++++++++++++ | 59% ~07s
|++++++++++++++++++++++++++++++ | 60% ~07s
|+++++++++++++++++++++++++++++++ | 61% ~07s
|+++++++++++++++++++++++++++++++ | 62% ~06s
|++++++++++++++++++++++++++++++++ | 63% ~06s
|++++++++++++++++++++++++++++++++ | 64% ~06s
|+++++++++++++++++++++++++++++++++ | 65% ~06s
|+++++++++++++++++++++++++++++++++ | 66% ~06s
|++++++++++++++++++++++++++++++++++ | 67% ~06s
|++++++++++++++++++++++++++++++++++ | 68% ~05s
|+++++++++++++++++++++++++++++++++++ | 69% ~05s
|+++++++++++++++++++++++++++++++++++ | 70% ~05s
|++++++++++++++++++++++++++++++++++++ | 71% ~05s
|++++++++++++++++++++++++++++++++++++ | 72% ~05s
|+++++++++++++++++++++++++++++++++++++ | 73% ~05s
|+++++++++++++++++++++++++++++++++++++ | 74% ~04s
|++++++++++++++++++++++++++++++++++++++ | 75% ~04s
|++++++++++++++++++++++++++++++++++++++ | 76% ~04s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~04s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~04s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~04s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~03s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~03s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~03s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~03s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=17s Calculating cluster 10
| | 0 % ~calculating
|+ | 1 % ~19s
|++ | 2 % ~19s
|++ | 3 % ~19s
|+++ | 4 % ~19s
|+++ | 5 % ~18s
|++++ | 6 % ~18s
|++++ | 7 % ~18s
|+++++ | 8 % ~18s
|+++++ | 9 % ~18s
|++++++ | 10% ~17s
|++++++ | 11% ~17s
|+++++++ | 12% ~17s
|+++++++ | 13% ~17s
|++++++++ | 14% ~17s
|++++++++ | 15% ~16s
|+++++++++ | 16% ~16s
|+++++++++ | 18% ~16s
|++++++++++ | 19% ~16s
|++++++++++ | 20% ~15s
|+++++++++++ | 21% ~15s
|+++++++++++ | 22% ~15s
|++++++++++++ | 23% ~15s
|++++++++++++ | 24% ~15s
|+++++++++++++ | 25% ~15s
|+++++++++++++ | 26% ~14s
|++++++++++++++ | 27% ~14s
|++++++++++++++ | 28% ~14s
|+++++++++++++++ | 29% ~14s
|+++++++++++++++ | 30% ~13s
|++++++++++++++++ | 31% ~13s
|++++++++++++++++ | 32% ~13s
|+++++++++++++++++ | 33% ~13s
|++++++++++++++++++ | 34% ~13s
|++++++++++++++++++ | 35% ~12s
|+++++++++++++++++++ | 36% ~12s
|+++++++++++++++++++ | 37% ~12s
|++++++++++++++++++++ | 38% ~12s
|++++++++++++++++++++ | 39% ~12s
|+++++++++++++++++++++ | 40% ~12s
|+++++++++++++++++++++ | 41% ~11s
|++++++++++++++++++++++ | 42% ~11s
|++++++++++++++++++++++ | 43% ~11s
|+++++++++++++++++++++++ | 44% ~11s
|+++++++++++++++++++++++ | 45% ~10s
|++++++++++++++++++++++++ | 46% ~10s
|++++++++++++++++++++++++ | 47% ~10s
|+++++++++++++++++++++++++ | 48% ~10s
|+++++++++++++++++++++++++ | 49% ~10s
|++++++++++++++++++++++++++ | 51% ~09s
|++++++++++++++++++++++++++ | 52% ~09s
|+++++++++++++++++++++++++++ | 53% ~09s
|+++++++++++++++++++++++++++ | 54% ~09s
|++++++++++++++++++++++++++++ | 55% ~09s
|++++++++++++++++++++++++++++ | 56% ~09s
|+++++++++++++++++++++++++++++ | 57% ~08s
|+++++++++++++++++++++++++++++ | 58% ~08s
|++++++++++++++++++++++++++++++ | 59% ~08s
|++++++++++++++++++++++++++++++ | 60% ~08s
|+++++++++++++++++++++++++++++++ | 61% ~08s
|+++++++++++++++++++++++++++++++ | 62% ~07s
|++++++++++++++++++++++++++++++++ | 63% ~07s
|++++++++++++++++++++++++++++++++ | 64% ~07s
|+++++++++++++++++++++++++++++++++ | 65% ~07s
|+++++++++++++++++++++++++++++++++ | 66% ~07s
|++++++++++++++++++++++++++++++++++ | 67% ~06s
|+++++++++++++++++++++++++++++++++++ | 68% ~06s
|+++++++++++++++++++++++++++++++++++ | 69% ~06s
|++++++++++++++++++++++++++++++++++++ | 70% ~06s
|++++++++++++++++++++++++++++++++++++ | 71% ~06s
|+++++++++++++++++++++++++++++++++++++ | 72% ~05s
|+++++++++++++++++++++++++++++++++++++ | 73% ~05s
|++++++++++++++++++++++++++++++++++++++ | 74% ~05s
|++++++++++++++++++++++++++++++++++++++ | 75% ~05s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~05s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~04s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~04s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~04s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~04s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~04s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~03s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~03s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~03s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~03s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~03s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=19s Calculating cluster 11
| | 0 % ~calculating
|+ | 1 % ~09s
|++ | 2 % ~08s
|++ | 3 % ~08s
|+++ | 5 % ~08s
|+++ | 6 % ~08s
|++++ | 7 % ~07s
|++++ | 8 % ~07s
|+++++ | 9 % ~07s
|++++++ | 10% ~07s
|++++++ | 11% ~07s
|+++++++ | 12% ~07s
|+++++++ | 14% ~07s
|++++++++ | 15% ~07s
|++++++++ | 16% ~06s
|+++++++++ | 17% ~06s
|++++++++++ | 18% ~06s
|++++++++++ | 19% ~06s
|+++++++++++ | 20% ~06s
|+++++++++++ | 22% ~06s
|++++++++++++ | 23% ~06s
|++++++++++++ | 24% ~06s
|+++++++++++++ | 25% ~06s
|++++++++++++++ | 26% ~06s
|++++++++++++++ | 27% ~06s
|+++++++++++++++ | 28% ~05s
|+++++++++++++++ | 30% ~05s
|++++++++++++++++ | 31% ~05s
|++++++++++++++++ | 32% ~05s
|+++++++++++++++++ | 33% ~05s
|++++++++++++++++++ | 34% ~05s
|++++++++++++++++++ | 35% ~05s
|+++++++++++++++++++ | 36% ~05s
|+++++++++++++++++++ | 38% ~05s
|++++++++++++++++++++ | 39% ~05s
|++++++++++++++++++++ | 40% ~05s
|+++++++++++++++++++++ | 41% ~05s
|++++++++++++++++++++++ | 42% ~04s
|++++++++++++++++++++++ | 43% ~04s
|+++++++++++++++++++++++ | 44% ~04s
|+++++++++++++++++++++++ | 45% ~04s
|++++++++++++++++++++++++ | 47% ~04s
|++++++++++++++++++++++++ | 48% ~04s
|+++++++++++++++++++++++++ | 49% ~04s
|+++++++++++++++++++++++++ | 50% ~04s
|++++++++++++++++++++++++++ | 51% ~04s
|+++++++++++++++++++++++++++ | 52% ~04s
|+++++++++++++++++++++++++++ | 53% ~04s
|++++++++++++++++++++++++++++ | 55% ~04s
|++++++++++++++++++++++++++++ | 56% ~03s
|+++++++++++++++++++++++++++++ | 57% ~03s
|+++++++++++++++++++++++++++++ | 58% ~03s
|++++++++++++++++++++++++++++++ | 59% ~03s
|+++++++++++++++++++++++++++++++ | 60% ~03s
|+++++++++++++++++++++++++++++++ | 61% ~03s
|++++++++++++++++++++++++++++++++ | 62% ~03s
|++++++++++++++++++++++++++++++++ | 64% ~03s
|+++++++++++++++++++++++++++++++++ | 65% ~03s
|+++++++++++++++++++++++++++++++++ | 66% ~03s
|++++++++++++++++++++++++++++++++++ | 67% ~03s
|+++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 69% ~02s
|++++++++++++++++++++++++++++++++++++ | 70% ~02s
|++++++++++++++++++++++++++++++++++++ | 72% ~02s
|+++++++++++++++++++++++++++++++++++++ | 73% ~02s
|+++++++++++++++++++++++++++++++++++++ | 74% ~02s
|++++++++++++++++++++++++++++++++++++++ | 75% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=08s Calculating cluster 12
| | 0 % ~calculating
|+ | 1 % ~15s
|++ | 2 % ~14s
|++ | 3 % ~14s
|+++ | 4 % ~14s
|+++ | 5 % ~14s
|++++ | 6 % ~13s
|++++ | 7 % ~13s
|+++++ | 9 % ~13s
|+++++ | 10% ~13s
|++++++ | 11% ~13s
|++++++ | 12% ~13s
|+++++++ | 13% ~12s
|+++++++ | 14% ~12s
|++++++++ | 15% ~12s
|++++++++ | 16% ~12s
|+++++++++ | 17% ~12s
|++++++++++ | 18% ~12s
|++++++++++ | 19% ~11s
|+++++++++++ | 20% ~11s
|+++++++++++ | 21% ~11s
|++++++++++++ | 22% ~11s
|++++++++++++ | 23% ~11s
|+++++++++++++ | 24% ~11s
|+++++++++++++ | 26% ~10s
|++++++++++++++ | 27% ~10s
|++++++++++++++ | 28% ~10s
|+++++++++++++++ | 29% ~10s
|+++++++++++++++ | 30% ~10s
|++++++++++++++++ | 31% ~10s
|++++++++++++++++ | 32% ~09s
|+++++++++++++++++ | 33% ~09s
|++++++++++++++++++ | 34% ~09s
|++++++++++++++++++ | 35% ~09s
|+++++++++++++++++++ | 36% ~09s
|+++++++++++++++++++ | 37% ~09s
|++++++++++++++++++++ | 38% ~09s
|++++++++++++++++++++ | 39% ~08s
|+++++++++++++++++++++ | 40% ~08s
|+++++++++++++++++++++ | 41% ~08s
|++++++++++++++++++++++ | 43% ~08s
|++++++++++++++++++++++ | 44% ~08s
|+++++++++++++++++++++++ | 45% ~08s
|+++++++++++++++++++++++ | 46% ~08s
|++++++++++++++++++++++++ | 47% ~08s
|++++++++++++++++++++++++ | 48% ~07s
|+++++++++++++++++++++++++ | 49% ~07s
|+++++++++++++++++++++++++ | 50% ~07s
|++++++++++++++++++++++++++ | 51% ~07s
|+++++++++++++++++++++++++++ | 52% ~07s
|+++++++++++++++++++++++++++ | 53% ~07s
|++++++++++++++++++++++++++++ | 54% ~06s
|++++++++++++++++++++++++++++ | 55% ~06s
|+++++++++++++++++++++++++++++ | 56% ~06s
|+++++++++++++++++++++++++++++ | 57% ~06s
|++++++++++++++++++++++++++++++ | 59% ~06s
|++++++++++++++++++++++++++++++ | 60% ~06s
|+++++++++++++++++++++++++++++++ | 61% ~06s
|+++++++++++++++++++++++++++++++ | 62% ~05s
|++++++++++++++++++++++++++++++++ | 63% ~05s
|++++++++++++++++++++++++++++++++ | 64% ~05s
|+++++++++++++++++++++++++++++++++ | 65% ~05s
|+++++++++++++++++++++++++++++++++ | 66% ~05s
|++++++++++++++++++++++++++++++++++ | 67% ~05s
|+++++++++++++++++++++++++++++++++++ | 68% ~04s
|+++++++++++++++++++++++++++++++++++ | 69% ~04s
|++++++++++++++++++++++++++++++++++++ | 70% ~04s
|++++++++++++++++++++++++++++++++++++ | 71% ~04s
|+++++++++++++++++++++++++++++++++++++ | 72% ~04s
|+++++++++++++++++++++++++++++++++++++ | 73% ~04s
|++++++++++++++++++++++++++++++++++++++ | 74% ~04s
|++++++++++++++++++++++++++++++++++++++ | 76% ~03s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~03s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~03s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~03s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~03s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 88% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=14s Calculating cluster 13
| | 0 % ~calculating
|+ | 1 % ~07s
|+ | 2 % ~07s
|++ | 3 % ~07s
|++ | 4 % ~07s
|+++ | 5 % ~07s
|+++ | 6 % ~07s
|++++ | 7 % ~07s
|++++ | 8 % ~07s
|+++++ | 9 % ~07s
|+++++ | 10% ~07s
|++++++ | 11% ~07s
|++++++ | 12% ~07s
|+++++++ | 13% ~07s
|+++++++ | 14% ~06s
|++++++++ | 15% ~06s
|++++++++ | 16% ~06s
|+++++++++ | 17% ~06s
|+++++++++ | 18% ~06s
|++++++++++ | 19% ~06s
|++++++++++ | 20% ~06s
|+++++++++++ | 21% ~06s
|+++++++++++ | 22% ~06s
|++++++++++++ | 23% ~06s
|++++++++++++ | 24% ~06s
|+++++++++++++ | 25% ~06s
|+++++++++++++ | 26% ~06s
|++++++++++++++ | 27% ~06s
|++++++++++++++ | 28% ~05s
|+++++++++++++++ | 29% ~05s
|+++++++++++++++ | 30% ~05s
|++++++++++++++++ | 31% ~05s
|++++++++++++++++ | 32% ~05s
|+++++++++++++++++ | 33% ~05s
|+++++++++++++++++ | 34% ~05s
|++++++++++++++++++ | 35% ~05s
|++++++++++++++++++ | 36% ~05s
|+++++++++++++++++++ | 37% ~05s
|+++++++++++++++++++ | 38% ~05s
|++++++++++++++++++++ | 39% ~05s
|++++++++++++++++++++ | 40% ~05s
|+++++++++++++++++++++ | 41% ~05s
|+++++++++++++++++++++ | 42% ~05s
|++++++++++++++++++++++ | 43% ~04s
|++++++++++++++++++++++ | 44% ~04s
|+++++++++++++++++++++++ | 45% ~04s
|+++++++++++++++++++++++ | 46% ~04s
|++++++++++++++++++++++++ | 47% ~04s
|++++++++++++++++++++++++ | 48% ~04s
|+++++++++++++++++++++++++ | 49% ~04s
|+++++++++++++++++++++++++ | 50% ~04s
|++++++++++++++++++++++++++ | 51% ~04s
|++++++++++++++++++++++++++ | 52% ~04s
|+++++++++++++++++++++++++++ | 53% ~04s
|+++++++++++++++++++++++++++ | 54% ~04s
|++++++++++++++++++++++++++++ | 55% ~04s
|++++++++++++++++++++++++++++ | 56% ~03s
|+++++++++++++++++++++++++++++ | 57% ~03s
|+++++++++++++++++++++++++++++ | 58% ~03s
|++++++++++++++++++++++++++++++ | 59% ~03s
|++++++++++++++++++++++++++++++ | 60% ~03s
|+++++++++++++++++++++++++++++++ | 61% ~03s
|+++++++++++++++++++++++++++++++ | 62% ~03s
|++++++++++++++++++++++++++++++++ | 63% ~03s
|++++++++++++++++++++++++++++++++ | 64% ~03s
|+++++++++++++++++++++++++++++++++ | 65% ~03s
|+++++++++++++++++++++++++++++++++ | 66% ~03s
|++++++++++++++++++++++++++++++++++ | 67% ~03s
|++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 69% ~02s
|+++++++++++++++++++++++++++++++++++ | 70% ~02s
|++++++++++++++++++++++++++++++++++++ | 71% ~02s
|++++++++++++++++++++++++++++++++++++ | 72% ~02s
|+++++++++++++++++++++++++++++++++++++ | 73% ~02s
|+++++++++++++++++++++++++++++++++++++ | 74% ~02s
|++++++++++++++++++++++++++++++++++++++ | 75% ~02s
|++++++++++++++++++++++++++++++++++++++ | 76% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=08s # optional: save the cluster markers
#write.csv(ClusterMarkers,"ClusterMarkers.csv")
See the top cluster markers
Now we can look at the cluster markers for cluster using EnrichR to compare to reference libraries
setEnrichrSite("Enrichr") # Human genesConnection changed to https://maayanlab.cloud/Enrichr/
Connection is Live!# list of all the databases
dbs <- listEnrichrDbs()
# this will list the possible libraries
dbs
# select libraries with cell types
db <- c('CellMarker_Augmented_2021','Azimuth_Cell_Types_2021')
Here is a small function to run easily on each cluster and find the cell type library predictions (specific to the libraries I selected)
checkCelltypes <- function(cluster_num = 0){
clusterX <- ClusterMarkers %>% filter(cluster == cluster_num & avg_log2FC > 0.25)
genes <- clusterX$gene
# the cell type libraries
# get the results for each library
clusterX.cell <- enrichr(genes, databases = db)
# visulize the results
print(plotEnrich(clusterX.cell[[1]], showTerms = 20, numChar = 40, y = "Count", orderBy = "P.value", title = 'CellMarker_Augmented_2021'))
print(plotEnrich(clusterX.cell[[2]], showTerms = 20, numChar = 40, y = "Count", orderBy = "P.value", title = 'Azimuth_Cell_Types_2021'))
}
Run the function for each cluster to see if we can identify cell types
cluster0 <- checkCelltypes(cluster_num = 0)Uploading data to Enrichr... Done.
Querying CellMarker_Augmented_2021... Done.
Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.
Cluster 0 is likely immature neurons - possibly both Glutamatergic and gabaergic
Cluster 1 is astrocytes
checkCelltypes(cluster_num = 11)Uploading data to Enrichr... Done.
Querying CellMarker_Augmented_2021... Done.
Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.
After we have looked at all the clusters we add manual annotations
levels(integrated_seurat)
[1] "0" "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13"Lets look at the annotations on the UMAP
DimPlot(integrated_seurat, group.by = "CellTypes", label = TRUE)
BREAK
Automated annotation We require reference data objects for both methods we will use
# developing forebrain
devforebrain <- readRDS("/Users/rhalenathomas/Documents/Data/scRNAseq/PublicData/Karolinski_DevForebrain_downsample_Level1.RDS")
# developing cortex
devcotex <- readRDS("/Users/rhalenathomas/Documents/Data/scRNAseq/PublicData/Nowakowski_dev_cortext.RDS")
# adult midbrain
midbrain <- readRDS("/Users/rhalenathomas/Documents/Data/scRNAseq/PublicData/KamathTotal_downsample.RDS")
#check the meta data
print("Developing Forebrain")[1] "Developing Forebrain"colnames(devforebrain@meta.data)[1] "orig.ident" "nCount_RNA" "nFeature_RNA" "Sample" "Level1" "Age"
[7] "Clusters" "New" "Celltypes" print("Developing cortex")[1] "Developing cortex"colnames(devcotex@meta.data) [1] "orig.ident" "nCount_RNA" "nFeature_RNA" "WGCNAcluster" "Name" "Age_in_Weeks"
[7] "RegionName" "Laminae" "Area" "Celltypes" print("Adult midbrain")[1] "Adult midbrain"colnames(midbrain@meta.data)[1] "orig.ident" "nCount_RNA" "nFeature_RNA"
[4] "Cell_Subtype" "Cell_Type" "disease__ontology_label"
[7] "organ__ontology_label" # we need to know the metadata slot name to use
Seurat label transfer using find anchors - predicts cell types from a reference Seurat object
scClassify R weighted kNN https://doi.org/10.15252/msb.20199389 https://sydneybiox.github.io/scClassify/articles/scClassify.html
We need to make the reference and query objects into a “dgCMatrix” object
length(query_clusters)
[1] 4028See the original cell type annotations
query_celltypes[1:10]
AAACCCAAGAGCTTTC-1_1 AAACCCACATTGACTG-1_1 AAACCCAGTTTGGAAA-1_1 AAACCCATCATCGACA-1_1
neurons_immature astrocytes_1 endothelial_2 astrocyte_2
AAACGAAAGCCTGAAG-1_1 AAACGAAAGGAGAATG-1_1 AAACGAACACGCGTGT-1_1 AAACGCTCACGTTCGG-1_1
endothelial_1 DAneurons neurons_mature neurons_mature
AAACGCTGTTGTCAGT-1_1 AAAGAACAGGTAGGCT-1_1
neurons_GABA neurons_mature
14 Levels: neurons_immature astrocytes_1 glia neurons_mature OPC ... DAneuronsRun scClassify
scClassify_res <- scClassify(exprsMat_train = dgCMat_ref,
cellTypes_train = ref_celltypes,
exprsMat_test = dgCMat_query,
cellTypes_test = query_celltypes,
tree = "HOPACH",
algorithm = "WKNN",
selectFeatures = c("limma"),
similarity = c("pearson"),
returnList = FALSE,
verbose = FALSE)Warning in asMethod(object) :
sparse->dense coercion: allocating vector of size 2.4 GiB
plotCellTypeTree(cellTypeTree(scClassify_res$trainRes))Warning: Removed 27 rows containing missing values (`geom_text()`).
See the cell type predictions by cluster
table(scClassify_res$testRes$test$pearson_WKNN_limma$predRes,query_celltypes)
query_celltypes
neurons_immature astrocytes_1 glia
EN 76 0 5
Endothelial 0 0 0
Glioblast 0 0 0
IN 320 0 0
Neuroblast 17 0 1
Neuroblast_IN_EN 141 0 3
Neuroblast_IN_EN_Neurons_U 8 0 0
Neuroblast_IN_EN_NPC_Endothelial_Neurons_U 0 0 0
Neuroblast_IN_EN_NPC_Neurons_U 0 0 0
Neurons 0 0 0
NPC 0 0 0
OPC 0 0 1
Pre-OPC 0 462 204
RG 0 2 66
RG_Glioblast 0 0 1
RG_Glioblast_OPC_Pre-OPC 0 0 1
RG_Glioblast_Pre-OPC 0 51 127
U 0 0 0
unassigned 4 3 29
VLMC 0 0 0
query_celltypes
neurons_mature OPC endothelial_1 endothelial_2
EN 18 7 9 178
Endothelial 0 0 0 0
Glioblast 0 1 7 2
IN 280 0 0 7
Neuroblast 0 1 1 2
Neuroblast_IN_EN 90 4 2 22
Neuroblast_IN_EN_Neurons_U 0 0 0 1
Neuroblast_IN_EN_NPC_Endothelial_Neurons_U 0 0 0 1
Neuroblast_IN_EN_NPC_Neurons_U 0 0 2 1
Neurons 0 0 0 1
NPC 0 0 0 0
OPC 0 6 0 0
Pre-OPC 0 171 23 0
RG 0 24 122 15
RG_Glioblast 0 7 30 3
RG_Glioblast_OPC_Pre-OPC 0 9 0 0
RG_Glioblast_Pre-OPC 0 53 12 0
U 0 0 0 0
unassigned 1 24 72 22
VLMC 0 0 0 0
query_celltypes
astrocyte_2 RadialGlia neurons1 neurons_GABA
EN 4 0 202 50
Endothelial 0 0 0 1
Glioblast 2 0 0 1
IN 0 0 0 80
Neuroblast 0 0 4 6
Neuroblast_IN_EN 3 2 11 50
Neuroblast_IN_EN_Neurons_U 0 0 8 0
Neuroblast_IN_EN_NPC_Endothelial_Neurons_U 0 0 0 0
Neuroblast_IN_EN_NPC_Neurons_U 0 0 0 2
Neurons 1 0 0 0
NPC 0 0 0 0
OPC 0 0 0 0
Pre-OPC 144 60 0 1
RG 19 89 0 3
RG_Glioblast 13 17 0 1
RG_Glioblast_OPC_Pre-OPC 5 1 0 0
RG_Glioblast_Pre-OPC 45 37 0 1
U 0 0 2 0
unassigned 17 13 0 12
VLMC 0 8 0 0
query_celltypes
neurons2 neural_stem DAneurons
EN 102 0 63
Endothelial 0 0 0
Glioblast 0 2 0
IN 4 2 0
Neuroblast 15 0 0
Neuroblast_IN_EN 64 0 3
Neuroblast_IN_EN_Neurons_U 1 0 0
Neuroblast_IN_EN_NPC_Endothelial_Neurons_U 0 0 0
Neuroblast_IN_EN_NPC_Neurons_U 3 0 2
Neurons 0 0 0
NPC 2 0 0
OPC 0 2 0
Pre-OPC 0 4 0
RG 0 61 0
RG_Glioblast 0 10 0
RG_Glioblast_OPC_Pre-OPC 0 0 0
RG_Glioblast_Pre-OPC 0 11 0
U 0 0 0
unassigned 1 6 2
VLMC 0 0 0Check another reference set
# refrence data
# we have the data prepared as a Seurat object
ref2 <- midbrain
ref2
#check the meta data
colnames(ref2@meta.data)
#make the reference matrix and reference cell types
dgCMat_ref2 <- GetAssayData(ref2)
# get the cell type data
Idents(ref2) <- "Cell_Type"
ref_celltypes2 <- Idents(ref2)
unique(ref_celltypes2)
# check the object
dim(dgCMat_ref2)
class(dgCMat_ref2)
# predict the cluster cell types from the second reference
scClassify_res <- scClassify(exprsMat_train = dgCMat_ref2,
cellTypes_train = ref_celltypes2,
exprsMat_test = dgCMat_query,
cellTypes_test = query_clusters,
tree = "HOPACH",
algorithm = "WKNN",
selectFeatures = c("limma"),
similarity = c("pearson"),
returnList = FALSE,
verbose = FALSE)
Sys.time()
plotCellTypeTree(cellTypeTree(scClassify_res$trainRes))
See the predictions by cluster
table(scClassify_res$testRes$test$pearson_WKNN_limma$predRes,query_clusters)
# reformat to see the top predictions for each cluster
pred_counts <- as.data.frame(table(query_clusters,scClassify_res$testRes$test$pearson_WKNN_limma$predRes))
pred_counts$Freq <- as.double(pred_counts$Freq)
head(pred_counts)
# see predictions by cluster in a table
top.pred <- as.data.frame(pred_counts %>% group_by(query_clusters) %>% top_n(2, Freq)) %>% arrange(query_clusters, desc(Freq))
top.pred
Add prediction annotations
Adjust annotations - merge clusters or not
---
title: "scRNAseq Workflow"
output: html_notebook
---

This workbook includes:
1. Creating a Seurat object from CellRanger output.
2. Preparing and cleaning the data
  a) Visualize QC
  b) Filter out unwanted cells
  c) Identify and remove doublets
  d) Normalization and scale
  e) Select Variable features
3. Merging and Harmonizing samples
  a) Merge samples
  b) Use Seurat find anchors to integrate
  c) Compare merged vs integrated
4. Dimensional reduction clustering and visualization
  a) PCA and component selection
  b) UMAP
  c) Clustering and visualization
5. Cluster annotation
  a) Visualize expression of known cell type markers
  b) Find cluster markers and look them up in reference cell type library
  c) Manual cluster annotation 
  d) Decisions on merging clusters
6. Automated cluster annotation
  a) Seurat label transfer
  b) scClassify


# Example data
We will use data from iPSC derived midbrain organoids
There are two samples from dissociated midbrain organoids
1) iPSC line from a patient with Parkinson's Disease carrying a triplication of the gene SNCA
2) The same iPSC line CRISPR corrected to make an isogenenic control


# Analysis workflow

Load your required libraries.
You need to have these libraries already installed. 

```{r}
Sys.time()
library(Seurat)
library(tidyverse)
library(DoubletFinder)
library(enrichR)
library(clustree)
library("scClassify")
library(SingleCellExperiment)
library("Matrix")


```


Load the data: Starting with the control data.

```{r}
# load data

# read in the data - CellRanger output - barcodes, features, expression matrix

# you need to enter the file path to the folder with the three files
con_data <- Read10X("/Users/rhalenathomas/Documents/Data/scRNAseq/AST23_BrainComm/CellRangerOuts/AST23isogenic/raw_feature_bc_matrix") 

#Look at the dimensions of the matrix
dim(con_data)

#Look at a small part of the data
con_data[1:5, 1:5]

#Look at the distribution of the number of UMIs per cell
colSums(con_data) %>% summary
#Look at the distribution of the number of genes per cell  
colSums(con_data > 0) %>% summary



```


Remove barcodes with too few genes that could be empty droplets

```{r}
#Remove barcodes with less than 100 genes detected (you can select a different value here)
# without 
con_data <- con_data[, colSums(con_data > 0)> 100]
dim(con_data)
colSums(con_data) %>% summary

```


Filter genes and create a Seurat object


```{r}
#We might not want to include genes that occur in few cells are no cells.  Here we will filter out genes/transcripts that are in less than 3 cells. 
# you don't have to filter any genes you can also change to any filter threshold you want

#Make a Seurat object
#Removing any genes detected in less than 3 cells

# we can also filter cells at this stage too. 
con_seu <- CreateSeuratObject(con_data, project = "Control", min.cells = 3)
# look at the object dimensions
con_seu

```


Data distribution
```{r}
# look at the distribution of total counts of RNA across cells
con_seu$nCount_RNA %>% summary

# look at the distribution of unique RNA transcripts across cells

con_seu$nFeature_RNA %>% summary

```


Visualize the distributions

```{r}

VlnPlot(con_seu, features = c("nCount_RNA","nFeature_RNA"), pt.size = 0)

```

Filter out unwanted cells

```{r}
# Example cell filtering based on mitochondrial count percentage and number of UMIs ----------

#Calculate the percentage of RNA encoded mitochondrial genes from the mitochondrial DNA
con_seu <- PercentageFeatureSet(con_seu, pattern = "^MT-", col.name = "percent.MT")
con_seu$percent.MT %>% summary

VlnPlot(con_seu, features = "percent.MT", pt.size = 0.001)

```
Now we will filter some cells with too high mitochondrial RNA
Filter out cells with too many RNA reads - these are likely doublets

```{r}


#Remove any cells with more than 20% mitochondrial counts
con_seu.ft <- subset(con_seu, percent.MT < 20)

#Remove cells with very high UMI counts, which may be possible multiplets
con_seu.ft <- subset(con_seu.ft, nCount_RNA < 20000)

# see the results
VlnPlot(con_seu.ft, features = c("percent.MT", "nCount_RNA", "nFeature_RNA"), pt.size = 0.001)

# check how many cells we have
con_seu.ft

VlnPlot(con_seu.ft, features = "nFeature_RNA", pt.size = 0.001, y.max = 1000)


```

We might want to filter more cells with low total and/or unique RNA

```{r}

# try some different filtering options
con_seu.ft <- subset(con_seu, percent.MT < 20)
dim(con_seu)
dim(con_seu.ft)


```

Apply final filtering conditions
```{r}

con_seu_ft <- subset(con_seu, nCount_RNA < 60000 & nFeature_RNA > 500 & 
                     percent.MT < 20)

dim(con_seu_ft)

```

Clear extra data object we don't need anymore

```{r}

rm(con_data,con_seu.ft)

```


Normalizing 

```{r}
# Normalize data (log normalization) and select genes with variable expression across cells --------------------------------------

con_seu_ft <- NormalizeData(con_seu_ft, normalization.method = "LogNormalize", scale.factor = 10000)

#Check out the effect of normalization
GetAssayData(con_seu_ft, assay = "RNA", slot = "data") %>% expm1 %>% colSums %>% head
GetAssayData(con_seu_ft, assay = "RNA", slot = "counts") %>% colSums %>% head

```

Finding Variable features 
```{r}
# three methods are available to choose variable features in this function
# our selection method is vst
con_seu_ft <- FindVariableFeatures(con_seu_ft, selection.method = "vst", nfeatures = 2000)


var  <- VariableFeatures(con_seu_ft)
VariableFeaturePlot(con_seu_ft)
var[1:10]



```

Dimensionality reduction PCA and UMAP

```{r}
#Scaling is recommended before PCA, as otherwise highly expressed genes will have a disproportionate effect on the PC composition

# we are also regressing MT genes to remove them from the PCA
con_seu_ft <- ScaleData(con_seu_ft, vars.to.regress = "percent.MT")
con_seu_ft@assays$RNA@scale.data %>% dim

#Linear dimensionality reduction
#Choosing the number of PCs can depend on how many cells you have
con_seu_ft <- RunPCA(con_seu_ft, assay = "RNA", npcs = 30)

PCAPlot(con_seu_ft)

#Assess how many PCs capture most of the information in the data 
ElbowPlot(con_seu_ft, ndims = 30)

```

We won't run this code
I've included this analysis that calculates the cut-off for signicance of component numbers.  However the function runs multiple iterations of the PCA and will take a long time to run. 

```{r}
# Jackstraw

#Assess how many PCs capture most of the information in the data 
seu <-JackStraw(seu, reduction = "pca",
  dims = 30)
seu <- ScoreJackStraw(seu, reduction = "pca", dims = 1:30)
JackStrawPlot(seu, dims = 1:30)

```


Non-linear dimensional reduction using UMAP
```{r}

#Non-linear dimensionality reduction
#Choosing how many PCs to input can depend on the elbow plot and on the number of cells
#There are many parameters that can e tweaked and optimized in a UMAP plot
#You can see some demos here: https://pair-code.github.io/understanding-umap/
con_seu_ft <- RunUMAP(con_seu_ft, dims = 1:18)
UMAPPlot(con_seu_ft)


```


Doublet identification

```{r}

# Assess possible doublets  -----------------------------------------------
#Using instructions here: https://github.com/chris-mcginnis-ucsf/

#First we have to find a pK which determines how big of a neighborhood will be examined for doublets
#This should be chosen for each library separately
#First we test a number of pN (proportion of generated artificial doublets) and pK
#We get different lists of probabilities of artifical nearest neighbors with these tested parameters
#Also keep in mind the results are not deterministic (every run will give slightly different results)
sweep.res.con <- paramSweep_v3(con_seu_ft, PCs = 1:18, sct = FALSE)

#We do not have the "ground truth" regarding doublets, such from from genotype data for pooled samples 
#We sumamrize the performance of the range of pN=pK parameters we tested
sweep.stats_con <- summarizeSweep(sweep.res.con, GT = FALSE)

#Here the "best" pK for the data is chosen based on a metric determined by the DoubletFinder developers
#Which performs best in datasets where the ground truth is known
bcmvn_con <- find.pK(sweep.stats_con)
ggplot(bcmvn_con, aes(x = pK, y = BCmetric, group = "Sweep")) + geom_point() + geom_line() + 
  theme(axis.text.x = element_text(angle = 90))

```


```{r}

#We will pick pK = 0.08
#We are not going to use our clustering information to estimate "homotypic" doublets
#We are simply going to use an expected doublet formation rate of 2.5% based on the number of starting cells loaded

nExp_poi <- round(0.025*nrow(con_seu_ft@meta.data))
con_seu_ft <- doubletFinder_v3(con_seu_ft, PCs = 1:18, pN = 0.25, pK = 0.08, nExp = nExp_poi, reuse.pANN = FALSE, sct = FALSE)

#Here we update the Seurat object version just in case the one returned by DoubletFinder is an older version
con_seu_ft <- UpdateSeuratObject(con_seu_ft)

# we have now identified doublets but we have not removed them


```

Visualize the doublet removal results

```{r}

# we need to look in the data object

#Visualize and assess the cells called as probable doublets
UMAPPlot(con_seu_ft, group.by = "DF.classifications_0.25_0.08_73")

# table of doublets and signlets
con_seu_ft$DF.classifications_0.25_0.08_73 %>% table

# visualize the features in doublets and singlets
VlnPlot(con_seu_ft, features = c("nCount_RNA", "nFeature_RNA", "percent.MT", "pANN_0.25_0.08_73"), 
        group.by = "DF.classifications_0.25_0.08_73", pt.size = 0.001, ncol = 2, log = TRUE)

```

```{r}
# remove the doublets
# we can do this by subset
# first we need to set the active meta data slot to the doublet identification
Idents(con_seu_ft) <- "DF.classifications_0.25_0.08_73"
# we select only the singlet cells
con_seu_ft2 <- subset(con_seu_ft, idents = "Singlet")
dim(con_seu_ft)
dim(con_seu_ft2)

```




Repeat the above steps for the SNCA triplication patient line

```{r}
# read in data

ast_data <- Read10X("/Users/rhalenathomas/Documents/Data/scRNAseq/AST23_BrainComm/CellRangerOuts/AST23/raw_feature_bc_matrix")


# create seurat object


# filter object with the same settings as with the control


# PCA analysis

# Remove doublets



```


```{r}
# clean up 
rm(ast_data,ast_seu_ft,bcmvn_ast,bcmvn_con,con_seu_ft, sweep.res.ast, sweep.res.con, sweep.stats_ast, sweep.stats_con)
```


# BREAK

Merge data objects

```{r}

merge_seurat <- merge(con_seu_ft2,ast_seu_ft2)
merge_seurat

unique(merge_seurat$orig.ident)


```

Find anchors between the two data objects
```{r}
sample.list <- SplitObject(merge_seurat, split.by = "orig.ident")

# We have already normalized and identified variable features in each sample
# If we had not done so we can normalize here
#for (i in 1:length(sample.list)){
 # org.list[[i]] <- NormalizeData(org.list[[i]], verbose = FALSE)
  #org.list[[i]] <- FindVariableFeatures(org.list[[i]], selection.method = "vst")
#}

# Now we find features that can act as anchors between the two samples
int.anchors <- FindIntegrationAnchors(object.list = sample.list, dims = 1:50)
integrated_seurat <- IntegrateData(anchorset = int.anchors, dims = 1:50)

```


Optional: save the integrated object or read in the Integrated object for the next step.

```{r}
# remove # comment from the code you want to run

saveRDS(integrated_seurat,"IntegratedSeurat.RDS")
#integrated_seurate <- readRDS("IntegratedSeurat.RDS")

```

PCA and UMAP on the merged object

```{r}
# merged object

DefaultAssay(merge_seurat) <- "RNA"

merge_seurat <- ScaleData(merge_seurat, verbose = FALSE)
# in the merge data set we sill need features for the PCA input
merge_seurat <- FindVariableFeatures(merge_seurat, selection.method = "vst")
merge_seurat <- RunPCA(merge_seurat, npcs = 30, verbose = FALSE)
merge_seurat <- RunUMAP(merge_seurat, reduction = "pca", dims = 1:30)


```



Repeat PCA and UMAP for the integrated object

```{r}
DefaultAssay(integrated_seurat) <- "integrated"
integrated_seurat <- ScaleData(integrated_seurat, verbose = FALSE)
# only the integrated features will be the pca input

integrated_seurat <- RunPCA(integrated_seurat, npcs = 30, verbose = FALSE)
integrated_seurat <- RunUMAP(integrated_seurat, reduction = "pca", dims = 1:30)

```


Optional: save the PCA and UMAP integrated object or read in the saved object
```{r}
# remove # comment from the code you want to run
saveRDS(integrated_seurat,"IntegratedSeuratGraphs.RDS")
#integrated_seurat <- readRDS("IntegratedSeuratGraphs.RDS")

```

Let's look at the UMAPs from the merged vs the integrated data
```{r}

p1 <- DimPlot(merge_seurat, group.by = "orig.ident") + ggtitle("Merge")
p2 <- DimPlot(integrated_seurat, group.by = "orig.ident") + ggtitle("Integrated")

p1
p2

```
We see almost no difference in this data. This is not the case in all data sets

Cluster the integrated data

```{r}
# see the importance of the pca components
ElbowPlot(integrated_seurat, ndims=30)
integrated_seurat

```

```{r}
dim(integrated_seurat)

```

We will choose 20 PCs
There are 4028 cells.  A common rule of thumb for choosing k for nearest neighbours is using the square root of the number of cells = 63

```{r}
# calculate the square root
sqrt(4028)

# the K parameter changes the size of clusters by changing the starting nodes input into the Louvain network

integrated_seurat <- FindNeighbors(integrated_seurat, dims = 1:20, k.param = 63)
# the number of clusters is dependent on the resolution a number from 0-2. 
# Higher values make more clusters
# we include 
integrated_seurat <- FindClusters(integrated_seurat, resolution = c(0,0.05,0.25,0.4,0.5,0.6,1,1.5) )

# we can visualize which cells are grouped together at different resolutions using clustree

clustree(integrated_seurat, prefix = "integrated_snn_res.")

```


Visualize the UMAP of the different cluster resolutions
```{r}
res <- c(0.05,0.25,0.4,0.5,0.6,1,1.5)
resolutions <- paste("integrated_snn_res.", res, sep="")
resolutions

for(r in resolutions){
  print(DimPlot(integrated_seurat, group.by = r))
}


```

# BREAK


Now we need to choose a resolution to annotate.
I will select resolution of 0.6.

```{r}
# Scale the total RNA
# before we only scaled the integrated expression for the genes used for integration
# now we want to scale all genes

DefaultAssay(integrated_seurat) <- "RNA"
integrated_seurat <- ScaleData(integrated_seurat)


```



Look at known cell type markers

```{r}
# features list from literature

da_neurons <- c("TH","SLC6A3","SLC18A2","SOX6","NDNF","SNCG","ALDH1A1","CALB1","TACR2","SLC17A6","SLC32A1","OTX2","GRP","LPL","CCK","VIP")
NPC_orStemLike <- c("DCX","NEUROD1","TBR1","PCNA","MKI67","SOX2","NES","PAX6","MASH1")
mature_neurons = c("RBFOX3","SYP","DLG45","VAMP1","VAMP2","TUBB3","SYT1","BSN","HOMER1","SLC17A6")
excitatory_neurons = c("GRIA2","GRIA1","GRIA4","GRIN1","GRIN2B","GRIN2A","GRIN3A","GRIN3","GRIP1","CAMK2A")
inhbitory_neurons = inh = c("GAD1","GAD2", "GAT1","PVALB","GABR2","GABR1","GBRR1","GABRB2","GABRB1","GABRB3","GABRA6","GABRA1","GABRA4","TRAK2")
astrocytes <- c("GFAP","S100B","AQP4","APOE", "SOX9","SLC1A3")
oligodendrocytes <- c("MBP","MOG","OLIG1","OLIG2","SOX10")
opc <- 
radial_glia <- c("PTPRC","AIF1","ADGRE1", "VIM", "TNC","PTPRZ1","FAM107A","HOPX","LIFR",
              "ITGB5","IL6ST","SLC1A3")
epithelial <- c("HES1","HES5","SOX2","SOX10","NES","CDH1","NOTCH1")

microglia <- c("IBA1","P2RY12","P2RY13","TREM119", "GPR34","SIGLECH","TREM2",
               "CX3CR1","FCRLS","OLFML3","HEXB","TGFBR1", "SALL1","MERTK",
               "PROS1")

features_list <- c("MKI67","SOX2","POU5F1","DLX2","PAX6","SOX9","HES1","NES","RBFOX3","MAP2","NCAM1","CD24","GRIA2","GRIN2B","GABBR1","GAD1","GAD2","GABRA1","GABRB2","TH","ALDH1A1","LMX1B","NR4A2","CORIN","CALB1","KCNJ6","CXCR4","ITGA6","SLC1A3","CD44","AQP4","S100B", "PDGFRA","OLIG2","MBP","CLDN11","VIM","VCAM1")

short_list <- c("MKI67","SOX9","HES1","NES","DLX2","RBFOX3","MAP2","TH","CALB1","KCNJ6","SLC1A3","CD44","AQP4","S100B","OLIG2","MBP","VIM")



```

Seurat has several helpful plotting function that use ggplot

```{r}
# we set the active identity of the meta data to be the clusters at the resolution we want to label
Idents(integrated_seurat) <- "integrated_snn_res.0.6"

FeaturePlot(integrated_seurat, label = TRUE, features = short_list)



```



```{r}
# this will let us see one at at time
for (i in short_list) {
  print(FeaturePlot(integrated_seurat, features = i, min.cutoff = 'q1', max.cutoff = 'q97', label = TRUE))
}


```
Now that we see the TH is all in one spot that is part of a large cluster we look back at the different cluster level.

```{r}

# see the difference between samples
FeaturePlot(integrated_seurat, features = "VIM", min.cutoff = 'q1', max.cutoff = 'q97', label = TRUE, split.by = "orig.ident")


# look at the Feature plots with the cluster resolution 1
Idents(integrated_seurat) <- "integrated_snn_res.1"
FeaturePlot(integrated_seurat, label = TRUE, features = c("VIM","AQP4"))

```


Dot Plots

```{r}

DotPlot(integrated_seurat, group.by = "integrated_snn_res.1", 
        features = short_list, assay = "RNA") + RotatedAxis()



DotPlot(integrated_seurat, group.by = "integrated_snn_res.1", 
        features = da_neurons, assay = "RNA") + RotatedAxis()

DotPlot(integrated_seurat, group.by = "integrated_snn_res.1", 
        features = mature_neurons, assay = "RNA") + RotatedAxis()


```

Heatmaps

```{r}


DoHeatmap(integrated_seurat, group.by = "integrated_snn_res.1", 
        features = short_list, slot = "scale.data")


```

Look at more expression lists

```{r}


```


Find Cluster markers

```{r}
# cluster markers will be calculated for the active identity

Idents(integrated_seurat) <- "integrated_snn_res.1"
ClusterMarkers <- FindAllMarkers(integrated_seurat, only.pos = TRUE)

# optional: save the cluster markers
#write.csv(ClusterMarkers,"ClusterMarkers.csv")



```

See the top cluster markers

```{r}
head(ClusterMarkers)
top5 <- ClusterMarkers %>% group_by(cluster) %>% top_n(n=5, wt =avg_log2FC)

top2 <- ClusterMarkers %>% group_by(cluster) %>% top_n(n=2, wt =avg_log2FC)
DoHeatmap(integrated_seurat, features = top5$gene, size = 3, angle = 90, group.by = "integrated_snn_res.1")

DoHeatmap(integrated_seurat, features = top2$gene, size = 3, angle = 90, group.by = "integrated_snn_res.1")

```

Now we can look at the cluster markers for cluster using EnrichR to compare to reference libraries

```{r}


setEnrichrSite("Enrichr") # Human genes
# list of all the databases

dbs <- listEnrichrDbs()

# this will list the possible libraries
dbs

# select libraries with cell types
db <- c('CellMarker_Augmented_2021','Azimuth_Cell_Types_2021')


```



Here is a small function to run easily on each cluster and find the cell type library predictions (specific to the libraries I selected)

```{r}

checkCelltypes <- function(cluster_num = 0){
  clusterX <- ClusterMarkers %>% filter(cluster == cluster_num & avg_log2FC > 0.25)
  genes <- clusterX$gene
  # the cell type libraries
  # get the results for each library
  clusterX.cell <- enrichr(genes, databases = db)
  # visualize the results
print(plotEnrich(clusterX.cell[[1]], showTerms = 20, numChar = 40, y = "Count", orderBy = "P.value", title = 'CellMarker_Augmented_2021'))
print(plotEnrich(clusterX.cell[[2]], showTerms = 20, numChar = 40, y = "Count", orderBy = "P.value", title = 'Azimuth_Cell_Types_2021'))

}


```

Run the function for each cluster to see if we can identify cell types

```{r}

cluster0 <- checkCelltypes(cluster_num = 0)

```
Cluster 0 is likely immature neurons - possibly both Glutamatergic and gabaergic

```{r}
cluster1 <- checkCelltypes(cluster_num = 1)

as.data.frame(cluster1$data)
cluster1[["data"]]


```
Cluster 1 is astrocytes

```{r}

checkCelltypes(cluster_num = 11)

```

After we have looked at all the clusters we add manual annotations


```{r}

# we need to set the identity to rename
Idents(integrated_seurat) <- "integrated_snn_res.1"

# we need to make a vector of the cell type in the same order - in the cluster order

cell_types1 <- c("neurons_immature", "astrocytes_1","glia",
                 "neurons_mature","OPC","endothelial_1",
                 "endothelial_2","astrocyte_2","RadialGlia",
                 "neurons1","neurons_GABA","neurons2","neural_stem","DAneurons")
  
names(cell_types1) <- levels(integrated_seurat)
integrated_seurat <- RenameIdents(integrated_seurat, cell_types1)
integrated_seurat <- AddMetaData(object=integrated_seurat, metadata=Idents(integrated_seurat), col.name = "CellTypes")


```


Lets look at the annotations on the UMAP

```{r}

DimPlot(integrated_seurat, group.by = "CellTypes", label = TRUE)

```


# BREAK


Automated annotation 
We require reference data objects for both methods we will use

```{r}

# developing forebrain
devforebrain <- readRDS("/Users/rhalenathomas/Documents/Data/scRNAseq/PublicData/Karolinski_DevForebrain_downsample_Level1.RDS")

# developing cortex

devcotex <- readRDS("/Users/rhalenathomas/Documents/Data/scRNAseq/PublicData/Nowakowski_dev_cortext.RDS")

# adult midbrain

midbrain <- readRDS("/Users/rhalenathomas/Documents/Data/scRNAseq/PublicData/KamathTotal_downsample.RDS")

#check the meta data
print("Developing Forebrain")
colnames(devforebrain@meta.data)
print("Developing cortex")
colnames(devcotex@meta.data)
print("Adult midbrain")
colnames(midbrain@meta.data)

# we need to know the metadata slot name to use


```

Seurat label transfer using find anchors - predicts cell types from a reference Seurat object

```{r}

# set the active meta data to be the cell type labels we want

Idents(devforebrain) <- "Celltypes"
# set the default assay to be RNA because those are the expression values we want
DefaultAssay(devforebrain) <- "RNA"
DefaultAssay(integrated_seurat) <- "RNA"


# find the reference anchors
anchors <- FindTransferAnchors(reference = devforebrain ,query = integrated_seurat, dims = 1:25)

# now we make predictions with the anchors
predictions <- TransferData(anchorset = anchors, refdata = devforebrain$Celltypes)

# look at the predictions output
head(predictions)

# add the predictions to the meta data
integrated_seurat <- AddMetaData(integrated_seurat, metadata = predictions$predicted.id, col.name = "predicted_ID")

# we can also consider the probability of each prediction
integrated_seurat$predicted_threshold <- ifelse(predictions$prediction.score.max > 0.75, integrated_seurat$predicted_ID, "None")

 
## check the proportion of cell types predicted in each cluster

t.lables <- as.data.frame(table(integrated_seurat$integrated_snn_res.1, 
                                integrated_seurat$predicted_ID))
t.lables$Freq <- as.double(t.lables$Freq)
ggplot(t.lables, aes(y = Freq, x = Var1, fill = Var2)) + geom_bar(position = "stack", stat= "identity")

# see predictions by cluster in a table
top.pred <- as.data.frame(t.lables  %>% group_by(Var1)  %>% top_n(2, Freq)) %>% arrange(Var1, desc(Freq))
top.pred



```




scClassify R weighted kNN https://doi.org/10.15252/msb.20199389
https://sydneybiox.github.io/scClassify/articles/scClassify.html

We need to make the reference and query objects into a "dgCMatrix" object

```{r}

ref <- devforebrain

ref$Level1 <- NULL

colnames(ref@meta.data)


# make a dfCMatrix from Seurat object to use in scClassify
Idents(ref) <- "Celltypes"

dgCMat_ref <- GetAssayData(ref)
# get the cell type data
Idents(ref) <- "Celltypes"
ref_celltypes <- Idents(ref)
unique(ref_celltypes)


# convert the integrated clustered object into dgCMatrix
DefaultAssay(integrated_seurat) <- "RNA"
dgCMat_query <- GetAssayData(integrated_seurat)

# get the meta data to group predictions by
# we will use the clusters ids 
# we could use the cell type annotations we made above

Idents(integrated_seurat) <- "integrated_snn_res.1"
query_clusters <- Idents(integrated_seurat)

Idents(integrated_seurat) <- "CellTypes"  
query_celltypes <- Idents(integrated_seurat)

length(query_clusters)
# check the objects
dim(dgCMat_ref)
dim(dgCMat_query)

class(dgCMat_ref)
class(dgCMat_query)

```

See the original cell type annotations
```{r}
table(ref_celltypes)
table(query_clusters)

length(ref_celltypes)
length(query_celltypes)

query_celltypes[1:10]


```

Run scClassify
```{r}

scClassify_res <- scClassify(exprsMat_train = dgCMat_ref,
                             cellTypes_train = ref_celltypes,
                             exprsMat_test = dgCMat_query,
                             cellTypes_test = query_celltypes,
                             tree = "HOPACH",
                             algorithm = "WKNN",
                             selectFeatures = c("limma"),
                             similarity = c("pearson"),
                             returnList = FALSE,
                             verbose = FALSE)



```

```{r}


plotCellTypeTree(cellTypeTree(scClassify_res$trainRes))


```



See the cell type predictions by cluster

```{r}

table(scClassify_res$testRes$test$pearson_WKNN_limma$predRes,query_clusters)
table(scClassify_res$testRes$test$pearson_WKNN_limma$predRes,query_celltypes)

```


Check another reference set

```{r}
# refrence data
# we have the data prepared as a Seurat object

ref2 <- midbrain
ref2

#check the meta data
colnames(ref2@meta.data)

#make the reference matrix and reference cell types 


dgCMat_ref2 <- GetAssayData(ref2)
# get the cell type data
Idents(ref2) <- "Cell_Type" 
ref_celltypes2 <- Idents(ref2)
unique(ref_celltypes2)

# check the object
dim(dgCMat_ref2)


class(dgCMat_ref2)



```

```{r}
# predict the cluster cell types from the second reference
scClassify_res <- scClassify(exprsMat_train = dgCMat_ref2,
                             cellTypes_train = ref_celltypes2,
                             exprsMat_test = dgCMat_query,
                             cellTypes_test = query_clusters,
                             tree = "HOPACH",
                             algorithm = "WKNN",
                             selectFeatures = c("limma"),
                             similarity = c("pearson"),
                             returnList = FALSE,
                             verbose = FALSE)
Sys.time()

```

```{r}

plotCellTypeTree(cellTypeTree(scClassify_res$trainRes))

```

See the predictions by cluster

```{r}
table(scClassify_res$testRes$test$pearson_WKNN_limma$predRes,query_clusters)



```

```{r}
# reformat to see the top predictions for each cluster

pred_counts <- as.data.frame(table(query_clusters,scClassify_res$testRes$test$pearson_WKNN_limma$predRes))

pred_counts$Freq <- as.double(pred_counts$Freq)

head(pred_counts)
# see predictions by cluster in a table
top.pred <- as.data.frame(pred_counts  %>% group_by(query_clusters)  %>% top_n(2, Freq)) %>% arrange(query_clusters, desc(Freq))
top.pred


```


Add prediction annotations


```{r}


```

Adjust annotations - merge clusters or not

```{r}


```




